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1

The Genographic Project Public Participation Mitochondrial DNA Database  

PubMed Central

The Genographic Project is studying the genetic signatures of ancient human migrations and creating an open-source research database. It allows members of the public to participate in a real-time anthropological genetics study by submitting personal samples for analysis and donating the genetic results to the database. We report our experience from the first 18 months of public participation in the Genographic Project, during which we have created the largest standardized human mitochondrial DNA (mtDNA) database ever collected, comprising 78,590 genotypes. Here, we detail our genotyping and quality assurance protocols including direct sequencing of the mtDNA HVS-I, genotyping of 22 coding-region SNPs, and a series of computational quality checks based on phylogenetic principles. This database is very informative with respect to mtDNA phylogeny and mutational dynamics, and its size allows us to develop a nearest neighbor–based methodology for mtDNA haplogroup prediction based on HVS-I motifs that is superior to classic rule-based approaches. We make available to the scientific community and general public two new resources: a periodically updated database comprising all data donated by participants, and the nearest neighbor haplogroup prediction tool. PMID:17604454

Behar, Doron M; Rosset, Saharon; Blue-Smith, Jason; Balanovsky, Oleg; Tzur, Shay; Comas, David; Mitchell, R. John; Quintana-Murci, Lluis; Tyler-Smith, Chris; Wells, R. Spencer

2007-01-01

2

A protocol for species delineation of public DNA databases, applied to the Insecta.  

PubMed

Public DNA databases are composed of data from many different taxa, although the taxonomic annotation on sequences is not always complete, which impedes the utilization of mined data for species-level applications. There is much ongoing work on species identification and delineation based on the molecular data itself, although applying species clustering to whole databases requires consolidation of results from numerous undefined gene regions, and introduces significant obstacles in data organization and computational load. In the current paper, we demonstrate an approach for species delineation of a sequence database. All DNA sequences for the insects were obtained and processed. After filtration of duplicated data, delineation of the database into species or molecular operational taxonomic units (MOTUs) followed a three-step process in which (i) the genetic loci L are partitioned, (ii) the species S are delineated within each locus, then (iii) species units are matched across loci to form the matrix L × S, a set of global (multilocus) species units. Partitioning the database into a set of homologous gene fragments was achieved by Markov clustering using edge weights calculated from the amount of overlap between pairs of sequences, then delineation of species units and assignment of species names were performed for the set of genes necessary to capture most of the species diversity. The complexity of computing pairwise similarities for species clustering was substantial at the cytochrome oxidase subunit I locus in particular, but made feasible through the development of software that performs pairwise alignments within the taxonomic framework, while accounting for the different ranks at which sequences are labeled with taxonomic information. Over 24 different homologs, the unidentified sequences numbered approximately 194,000, containing 41,525 species IDs (98.7% of all found in the insect database), and were grouped into 59,173 single-locus MOTUs by hierarchical clustering under parameters optimized independently for each locus. Species units from different loci were matched using a multipartite matching algorithm to form multilocus species units with minimal incongruence between loci. After matching, the insect database as represented by these 24 loci was found to be composed of 78,091 species units in total. 38,574 of these units contained only species labeled data, 34,891 contained only unlabeled data, leaving 4,626 units composed both of labeled and unlabeled sequences. In addition to giving estimates of species diversity of sequence repositories, the protocol developed here will facilitate species-level applications of modern-day sequence data sets. In particular, the L × S matrix represents a post-taxonomic framework that can be used for species-level organization of metagenomic data, and incorporation of these methods into phylogenetic pipelines will yield matrices more representative of species diversity. PMID:24929897

Chesters, Douglas; Zhu, Chao-Dong

2014-09-01

3

The National DNA Database  

Microsoft Academic Search

Over the last two years the Forensic Science Service (FSS) has developed and put into operation a National DNA Database that has analysed samples from individuals suspected of crime and stains from scenes of crime. It has provided more than 2200 links between individuals and scenes and 1200 links between scenes of crime. It uses an STR SGM (second generation

David J Werrett

1997-01-01

4

Enhancing the DNA Patent Database  

SciTech Connect

Final Report on Award No. DE-FG0201ER63171 Principal Investigator: LeRoy B. Walters February 18, 2008 This project successfully completed its goal of surveying and reporting on the DNA patenting and licensing policies at 30 major U.S. academic institutions. The report of survey results was published in the January 2006 issue of Nature Biotechnology under the title “The Licensing of DNA Patents by US Academic Institutions: An Empirical Survey.” Lori Pressman was the lead author on this feature article. A PDF reprint of the article will be submitted to our Program Officer under separate cover. The project team has continued to update the DNA Patent Database on a weekly basis since the conclusion of the project. The database can be accessed at dnapatents.georgetown.edu. This database provides a valuable research tool for academic researchers, policymakers, and citizens. A report entitled Reaping the Benefits of Genomic and Proteomic Research: Intellectual Property Rights, Innovation, and Public Health was published in 2006 by the Committee on Intellectual Property Rights in Genomic and Protein Research and Innovation, Board on Science, Technology, and Economic Policy at the National Academies. The report was edited by Stephen A. Merrill and Anne-Marie Mazza. This report employed and then adapted the methodology developed by our research project and quoted our findings at several points. (The full report can be viewed online at the following URL: http://www.nap.edu/openbook.php?record_id=11487&page=R1). My colleagues and I are grateful for the research support of the ELSI program at the U.S. Department of Energy.

Walters, LeRoy B.

2008-02-18

5

Characterization of new Schistosoma mansoni microsatellite loci in sequences obtained from public DNA databases and microsatellite enriched genomic libraries  

Microsoft Academic Search

In the last decade microsatellites have become one of the most useful genetic markers used in a large number of organisms due to their abundance and high level of polymorphism. Microsatellites have been used for individual identification, paternity tests, forensic studies and population genetics. Data on microsatellite abundance comes preferentially from microsatellite enriched libraries and DNA sequence databases. We have

NB Rodrigues; PT LoVerde; AJ Romanha; G Oliveira

2002-01-01

6

Compressing DNA sequence databases with coil  

PubMed Central

Background Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip) compression – an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. Results We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression – the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST) data. Finally, coil can efficiently encode incremental additions to a sequence database. Conclusion coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work. PMID:18489794

White, W Timothy J; Hendy, Michael D

2008-01-01

7

Database Support for Research in Public Administration  

ERIC Educational Resources Information Center

This study examines the extent to which databases support student and faculty research in the area of public administration. A list of journals in public administration, public policy, political science, public budgeting and finance, and other related areas was compared to the journal content list of six business databases. These databases…

Tucker, James Cory

2005-01-01

8

Characterization of new Schistosoma mansoni microsatellite loci in sequences obtained from public DNA databases and microsatellite enriched genomic libraries.  

PubMed

In the last decade microsatellites have become one of the most useful genetic markers used in a large number of organisms due to their abundance and high level of polymorphism. Microsatellites have been used for individual identification, paternity tests, forensic studies and population genetics. Data on microsatellite abundance comes preferentially from microsatellite enriched libraries and DNA sequence databases. We have conducted a search in GenBank of more than 16,000 Schistosoma mansoni ESTs and 42,000 BAC sequences. In addition, we obtained 300 sequences from CA and AT microsatellite enriched genomic libraries. The sequences were searched for simple repeats using the RepeatMasker software. Of 16,022 ESTs, we detected 481 (3%) sequences that contained 622 microsatellites (434 perfect, 164 imperfect and 24 compounds). Of the 481 ESTs, 194 were grouped in 63 clusters containing 2 to 15 ESTs per cluster. Polymorphisms were observed in 16 clusters. The 287 remaining ESTs were orphan sequences. Of the 42,017 BAC end sequences, 1,598 (3.8%) contained microsatellites (2,335 perfect, 287 imperfect and 79 compounds). The 1,598 BAC end sequences 80 were grouped into 17 clusters containing 3 to 17 BAC end sequences per cluster. Microsatellites were present in 67 out of 300 sequences from microsatellite enriched libraries (55 perfect, 38 imperfect and 15 compounds). From all of the observed loci 55 were selected for having the longest perfect repeats and flanking regions that allowed the design of primers for PCR amplification. Additionally we describe two new polymorphic microsatellite loci. PMID:12426598

Rodrigues, N B; Loverde, P T; Romanha, A J; Oliveira, G

2002-01-01

9

Criminal DNA databases: the European situation  

Microsoft Academic Search

In the last 5 years, a number of European countries have successfully introduced national databases holding the DNA profiles from suspected and convicted criminal offenders as well as from biological stain materials from unsolved crime cases. At present, DNA databases are fully or partially in operation in the UK, The Netherlands, Austria, Germany, Finland, Norway, Denmark, Switzerland and Sweden. Furthermore,

Peter M. Schneider; Peter D. Martin

2001-01-01

10

Forensic DNA Profiling and Database  

PubMed Central

The incredible power of DNA technology as an identification tool had brought a tremendous change in crimnal justice . DNA data base is an information resource for the forensic DNA typing community with details on commonly used short tandem repeat (STR) DNA markers. This article discusses the essential steps in compilation of COmbined DNA Index System (CODIS) on validated polymerase chain amplified STRs and their use in crime detection. PMID:23386793

Panneerchelvam, S.; Norazmi, M.N.

2003-01-01

11

Publications of Australian LIS Academics in Databases  

ERIC Educational Resources Information Center

This paper examines aspects of journal articles published from 1967 to 2008, located in eight databases, and authored or co-authored by academics serving for at least two years in Australian LIS programs from 1959 to 2008. These aspects are: inclusion of publications in databases, publications in journals, authorship characteristics of…

Wilson, Concepcion S.; Boell, Sebastian K.; Kennan, Mary Anne; Willard, Patricia

2011-01-01

12

Plant rDNA database: update and new features  

PubMed Central

The Plant rDNA database (www.plantrdnadatabase.com) is an open access online resource providing detailed information on numbers, structures and positions of 5S and 18S-5.8S-26S (35S) ribosomal DNA loci. The data have been obtained from >600 publications on plant molecular cytogenetics, mostly based on fluorescent in situ hybridization (FISH). This edition of the database contains information on 1609 species derived from 2839 records, which means an expansion of 55.76 and 94.45%, respectively. It holds the data for angiosperms, gymnosperms, bryophytes and pteridophytes available as of June 2013. Information from publications reporting data for a single rDNA (either 5S or 35S alone) and annotation regarding transcriptional activity of 35S loci now appears in the database. Preliminary analyses suggest greater variability in the number of rDNA loci in gymnosperms than in angiosperms. New applications provide ideograms of the species showing the positions of rDNA loci as well as a visual representation of their genome sizes. We have also introduced other features to boost the usability of the Web interface, such as an application for convenient data export and a new section with rDNA–FISH-related information (mostly detailing protocols and reagents). In addition, we upgraded and/or proofread tabs and links and modified the website for a more dynamic appearance. This manuscript provides a synopsis of these changes and developments. Database URL: http://www.plantrdnadatabase.com PMID:24980131

Garcia, Sònia; Gálvez, Francisco; Gras, Airy; Kova?ík, Aleš; Garnatje, Teresa

2014-01-01

13

Publication Kind Codes in STN Patent Databases  

E-print Network

Publication Kind Codes in STN Patent Databases Dokumentenart-Codes in STN-Patentdatenbanken Imprint Abstracts (CAPLUS), Chemical Abstracts (CAPLUS), Derwent World Patents Index (DWPI), and Derwent World Patents Index (DWPI)und INPADOCDB INPADOCDB international patent databases, together with a short

Hoffmann, Armin

14

Faculty Publications Databases in Academic Health Sciences Libraries  

Microsoft Academic Search

A survey of 172 academic health sciences libraries was conducted to determine how many have databases of faculty publications and what their databases are like. Of 128 respondents, only thirty-two have faculty publications databases. The majority of those who have them maintain comprehensive databases using commercial bibliographic software running on individual workstations. Only two institutions maintain databases containing exclusively journal

Renee Mansheim; JoLinda L. Thompson

1995-01-01

15

An integrated web medicinal materials DNA database: MMDBD (Medicinal Materials DNA Barcode Database)  

PubMed Central

Background Thousands of plants and animals possess pharmacological properties and there is an increased interest in using these materials for therapy and health maintenance. Efficacies of the application is critically dependent on the use of genuine materials. For time to time, life-threatening poisoning is found because toxic adulterant or substitute is administered. DNA barcoding provides a definitive means of authentication and for conducting molecular systematics studies. Owing to the reduced cost in DNA authentication, the volume of the DNA barcodes produced for medicinal materials is on the rise and necessitates the development of an integrated DNA database. Description We have developed an integrated DNA barcode multimedia information platform- Medicinal Materials DNA Barcode Database (MMDBD) for data retrieval and similarity search. MMDBD contains over 1000 species of medicinal materials listed in the Chinese Pharmacopoeia and American Herbal Pharmacopoeia. MMDBD also contains useful information of the medicinal material, including resources, adulterant information, medical parts, photographs, primers used for obtaining the barcodes and key references. MMDBD can be accessed at http://www.cuhk.edu.hk/icm/mmdbd.htm. Conclusions This work provides a centralized medicinal materials DNA barcode database and bioinformatics tools for data storage, analysis and exchange for promoting the identification of medicinal materials. MMDBD has the largest collection of DNA barcodes of medicinal materials and is a useful resource for researchers in conservation, systematic study, forensic and herbal industry. PMID:20576098

2010-01-01

16

24 CFR 81.72 - Public-use database and public information.  

Code of Federal Regulations, 2011 CFR

...2011-04-01 false Public-use database and public information. 81.72 ...Information § 81.72 Public-use database and public information. (a) General...available for public use, a public-use database containing public data as defined...

2011-04-01

17

24 CFR 81.72 - Public-use database and public information.  

Code of Federal Regulations, 2013 CFR

...2013-04-01 false Public-use database and public information. 81.72 ...Information § 81.72 Public-use database and public information. (a) General...available for public use, a public-use database containing public data as defined...

2013-04-01

18

24 CFR 81.72 - Public-use database and public information.  

Code of Federal Regulations, 2010 CFR

...2010-04-01 false Public-use database and public information. 81.72 ...Information § 81.72 Public-use database and public information. (a) General...available for public use, a public-use database containing public data as defined...

2010-04-01

19

24 CFR 81.72 - Public-use database and public information.  

Code of Federal Regulations, 2012 CFR

...2012-04-01 false Public-use database and public information. 81.72 ...Information § 81.72 Public-use database and public information. (a) General...available for public use, a public-use database containing public data as defined...

2012-04-01

20

24 CFR 81.72 - Public-use database and public information.  

Code of Federal Regulations, 2014 CFR

...2014-04-01 false Public-use database and public information. 81.72 ...Information § 81.72 Public-use database and public information. (a) General...available for public use, a public-use database containing public data as defined...

2014-04-01

21

Angiosperm DNA C-Values Database  

NSDL National Science Digital Library

The 1992 Global Convention on Biological Diversity (Rio de Janeiro) specified the need to make biodiversity data available "despite imperfections, rather than holding back information until more polished products are completed." Few organizations have done so. This Royal Botanic Gardens (Kew, UK) genome biodiversity database is one valuable exception. Founded in 1759, the Royal Botanic Gardens, Kew has built its unique collections which now include 6 million dried plant specimens - covering 90% of the world's plant species; 40,000 living plant taxa - estimated as 10% of the world's flora; and 80,000 fungi and artifacts of plant origin. Known best among botanists as a global resource for definitively identifying, classifying, and naming plants and fungi, Kew also maintains this database on DNA C-values. To access this free, searchable database, the user must provide an email address as well as the genus of interest; search results include Taxon, Family, 4C DNA amount (pg), and entry number/reference citation, listed separately for each species.

22

DNA HYBRIDIZATION AS A SIMILARITY CRITERION FOR QUERYING DIGITAL SIGNALS STORED IN DNA DATABASES  

E-print Network

DNA HYBRIDIZATION AS A SIMILARITY CRITERION FOR QUERYING DIGITAL SIGNALS STORED IN DNA DATABASES S USA ABSTRACT We demonstrate via simulation that hybridization of DNA molecules can be used as a similarity criterion for retrieving digital signals encoded and stored in a synthesized DNA database. After

Tsaftaris, Sotirios

23

The Availability of Faculty Publication Databases from Library Web Pages  

ERIC Educational Resources Information Center

Faculty publication databases or author bibliographies offer libraries an opportunity to provide services to users. Initially, these databases remained initiatives of special libraries in the health-sciences fields. Librarians used the publication information derived from these databases to compile lists for annual reports. However, the advent of…

Blummer, Barbara A.

2007-01-01

24

ALFRED: an allele frequency database for diverse populations and DNA polymorphisms  

PubMed Central

We have developed a publicly accessible database (ALFRED, the ALlele FREquency Database) that catalogues allele frequency data for a wide range of population samples and DNA polymorphisms. This database is web-accessible through our laboratory (Kidd Lab) Web site: http://info.med.yale.edu/genetics/kkidd . ALFRED currently contains data on 60 populations and 156 genetic systems including single nucleotide polymorphisms (SNPs), short tandem repeat polymorphisms (STRPs), variable number of tandem repeats (VNTRs) and insertion–deletion polymorphisms. While data are not available for all population–DNA polymorphism combinations, over 2000 allele frequency tables have been entered. Our database is designed (i) to address our specific research requirements as well as broader scientific objectives; (ii) to allow researchers and interested educators to easily navigate and retrieve data of interest to them; and (iii) to integrate links to other related public databases such as dbSNP, GenBank and PubMed. PMID:10592274

Cheung, Kei-Hoi; Osier, Michael V.; Kidd, Judith R.; Pakstis, Andrew J.; Miller, Perry L.; Kidd, Kenneth K.

2000-01-01

25

76 FR 1137 - Publicly Available Consumer Product Safety Information Database: Notice of Public Web Conferences  

Federal Register 2010, 2011, 2012, 2013, 2014

...Information Database: Notice of Public Web Conferences AGENCY: Consumer Product Safety...or ``we'') is announcing two Web conferences to demonstrate to interested...information database (``Database''). The Web conferences will be webcast live from...

2011-01-07

26

[Integrated DNA barcoding database for identifying Chinese animal medicine].  

PubMed

In order to construct an integrated DNA barcoding database for identifying Chinese animal medicine, the authors and their cooperators have completed a lot of researches for identifying Chinese animal medicines using DNA barcoding technology. Sequences from GenBank have been analyzed simultaneously. Three different methods, BLAST, barcoding gap and Tree building, have been used to confirm the reliabilities of barcode records in the database. The integrated DNA barcoding database for identifying Chinese animal medicine has been constructed using three different parts: specimen, sequence and literature information. This database contained about 800 animal medicines and the adulterants and closely related species. Unknown specimens can be identified by pasting their sequence record into the window on the ID page of species identification system for traditional Chinese medicine (www. tcmbarcode. cn). The integrated DNA barcoding database for identifying Chinese animal medicine is significantly important for animal species identification, rare and endangered species conservation and sustainable utilization of animal resources. PMID:25244735

Shi, Lin-Chun; Yao, Hui; Xie, Li-Fang; Zhu, Ying-Jie; Song, Jing-Yuan; Zhang, Hui; Chen, Shi-Lin

2014-06-01

27

Exploration of the Chemical Space of Public Genomic Databases  

EPA Science Inventory

The current project aims to chemically index the content of public genomic databases to make these data accessible in relation to other publicly available, chemically-indexed toxicological information. ...

28

Searching mixed DNA profiles directly against profile databases.  

PubMed

DNA databases have revolutionised forensic science. They are a powerful investigative tool as they have the potential to identify persons of interest in criminal investigations. Routinely, a DNA profile generated from a crime sample could only be searched for in a database of individuals if the stain was from single contributor (single source) or if a contributor could unambiguously be determined from a mixed DNA profile. This meant that a significant number of samples were unsuitable for database searching. The advent of continuous methods for the interpretation of DNA profiles offers an advanced way to draw inferential power from the considerable investment made in DNA databases. Using these methods, each profile on the database may be considered a possible contributor to a mixture and a likelihood ratio (LR) can be formed. Those profiles which produce a sufficiently large LR can serve as an investigative lead. In this paper empirical studies are described to determine what constitutes a large LR. We investigate the effect on a database search of complex mixed DNA profiles with contributors in equal proportions with dropout as a consideration, and also the effect of an incorrect assignment of the number of contributors to a profile. In addition, we give, as a demonstration of the method, the results using two crime samples that were previously unsuitable for database comparison. We show that effective management of the selection of samples for searching and the interpretation of the output can be highly informative. PMID:24528588

Bright, Jo-Anne; Taylor, Duncan; Curran, James; Buckleton, John

2014-03-01

29

Database Connects Public to University of Nebraska Research  

E-print Network

Database Connects Public to University of Nebraska Research By Steve Ress There's a wealth of water easier. An easily accessible and searchable database sponsored by the University of Nebraska Rachael Herpel, outreach and education specialist at the UNL Water Center. The database can be found

Nebraska-Lincoln, University of

30

Mock jurors' use of error rates in DNA database trawls.  

PubMed

Forensic science is not infallible, as data collected by the Innocence Project have revealed. The rate at which errors occur in forensic DNA testing-the so-called "gold standard" of forensic science-is not currently known. This article presents a Bayesian analysis to demonstrate the profound impact that error rates have on the probative value of a DNA match. Empirical evidence on whether jurors are sensitive to this effect is equivocal: Studies have typically found they are not, while a recent, methodologically rigorous study found that they can be. This article presents the results of an experiment that examined this issue within the context of a database trawl case in which one DNA profile was tested against a multitude of profiles. The description of the database was manipulated (i.e., "medical" or "offender" database, or not specified) as was the rate of error (i.e., one-in-10 or one-in-1,000). Jury-eligible participants were nearly twice as likely to convict in the offender database condition compared to the condition not specified. The error rates did not affect verdicts. Both factors, however, affected the perception of the defendant's guilt, in the expected direction, although the size of the effect was meager compared to Bayesian prescriptions. The results suggest that the disclosure of an offender database to jurors might constitute prejudicial evidence, and calls for proficiency testing in forensic science as well as training of jurors are echoed. PMID:23855323

Scurich, Nicholas; John, Richard S

2013-12-01

31

Enhancing thermal video using a public database of images  

NASA Astrophysics Data System (ADS)

We presented a system to display nightime imagery with natural colors using a public database of images. We initially combined two spectral bands of images, thermal and visible, to enhance night vision imagery, however the fused image gave an unnatural color appearance. Therefore, a color transfer based on look-up table (LUT) was used to replace the false color appearance with a colormap derived from a daytime reference image obtained from a public database using the GPS coordinates of the vehicle. Because of the computational demand in deriving the colormap from the reference image, we created an additional local database of colormaps. Reference images from the public database were compared to a compact local database to retrieve one of a limited number of colormaps that represented several driving environments. Each colormap in the local database was stored with an image from which it was derived. To retrieve a colormap, we compared the histogram of the fused image with histograms of images in the local database. The colormaps of the best match was then used for the fused image. Continuously selecting and applying colormaps using this approach offered a convenient way to color night vision imagery.

Qadir, Hemin; Kozaitis, S. P.; Ali, Ehsan

2014-05-01

32

DNAVaxDB: the first web-based DNA vaccine database and its data analysis  

PubMed Central

Since the first DNA vaccine studies were done in the 1990s, thousands more studies have followed. Here we report the development and analysis of DNAVaxDB (http://www.violinet.org/dnavaxdb), the first publically available web-based DNA vaccine database that curates, stores, and analyzes experimentally verified DNA vaccines, DNA vaccine plasmid vectors, and protective antigens used in DNA vaccines. All data in DNAVaxDB are annotated from reliable resources, particularly peer-reviewed articles. Among over 140 DNA vaccine plasmids, some plasmids were more frequently used in one type of pathogen than others; for example, pCMVi-UB for G- bacterial DNA vaccines, and pCAGGS for viral DNA vaccines. Presently, over 400 DNA vaccines containing over 370 protective antigens from over 90 infectious and non-infectious diseases have been curated in DNAVaxDB. While extracellular and bacterial cell surface proteins and adhesin proteins were frequently used for DNA vaccine development, the majority of protective antigens used in Chlamydophila DNA vaccines are localized to the inner portion of the cell. The DNA vaccine priming, other vaccine boosting vaccination regimen has been widely used to induce protection against infection of different pathogens such as HIV. Parasitic and cancer DNA vaccines were also systematically analyzed. User-friendly web query and visualization interfaces are available in DNAVaxDB for interactive data search. To support data exchange, the information of DNA vaccines, plasmids, and protective antigens is stored in the Vaccine Ontology (VO). DNAVaxDB is targeted to become a timely and vital source of DNA vaccines and related data and facilitate advanced DNA vaccine research and development. PMID:25104313

2014-01-01

33

Choice of population database for forensic DNA profile analysis  

PubMed Central

When evaluating the weight of evidence (WoE) for an individual to be a contributor to a DNA sample, an allele frequency database is required. The allele frequencies are needed to inform about genotype probabilities for unknown contributors of DNA to the sample. Typically databases are available from several populations, and a common practice is to evaluate the WoE using each available database for each unknown contributor. Often the most conservative WoE (most favourable to the defence) is the one reported to the court. However the number of human populations that could be considered is essentially unlimited and the number of contributors to a sample can be large, making it impractical to perform every possible WoE calculation, particularly for complex crime scene profiles. We propose instead the use of only the database that best matches the ancestry of the queried contributor, together with a substantial FST adjustment. To investigate the degree of conservativeness of this approach, we performed extensive simulations of one- and two-contributor crime scene profiles, in the latter case with, and without, the profile of the second contributor available for the analysis. The genotypes were simulated using five population databases, which were also available for the analysis, and evaluations of WoE using our heuristic rule were compared with several alternative calculations using different databases. Using FST = 0.03, we found that our heuristic gave WoE more favourable to the defence than alternative calculations in well over 99% of the comparisons we considered; on average the difference in WoE was just under 0.2 bans (orders of magnitude) per locus. The degree of conservativeness of the heuristic rule can be adjusted through the FST value. We propose the use of this heuristic for DNA profile WoE calculations, due to its ease of implementation, and efficient use of the evidence while allowing a flexible degree of conservativeness. PMID:25498938

Steele, Christopher D.; Balding, David J.

2014-01-01

34

Choice of population database for forensic DNA profile analysis.  

PubMed

When evaluating the weight of evidence (WoE) for an individual to be a contributor to a DNA sample, an allele frequency database is required. The allele frequencies are needed to inform about genotype probabilities for unknown contributors of DNA to the sample. Typically databases are available from several populations, and a common practice is to evaluate the WoE using each available database for each unknown contributor. Often the most conservative WoE (most favourable to the defence) is the one reported to the court. However the number of human populations that could be considered is essentially unlimited and the number of contributors to a sample can be large, making it impractical to perform every possible WoE calculation, particularly for complex crime scene profiles. We propose instead the use of only the database that best matches the ancestry of the queried contributor, together with a substantial FST adjustment. To investigate the degree of conservativeness of this approach, we performed extensive simulations of one- and two-contributor crime scene profiles, in the latter case with, and without, the profile of the second contributor available for the analysis. The genotypes were simulated using five population databases, which were also available for the analysis, and evaluations of WoE using our heuristic rule were compared with several alternative calculations using different databases. Using FST=0.03, we found that our heuristic gave WoE more favourable to the defence than alternative calculations in well over 99% of the comparisons we considered; on average the difference in WoE was just under 0.2 bans (orders of magnitude) per locus. The degree of conservativeness of the heuristic rule can be adjusted through the FST value. We propose the use of this heuristic for DNA profile WoE calculations, due to its ease of implementation, and efficient use of the evidence while allowing a flexible degree of conservativeness. PMID:25498938

Steele, Christopher D; Balding, David J

2014-12-01

35

Toward Privacy in Public Databases Shuchi Chawla1  

E-print Network

Toward Privacy in Public Databases Shuchi Chawla1 , Cynthia Dwork2 , Frank McSherry2 , Adam Smith3,mcsherry}@microsoft.com 3 Weizmann Institute of Science, adam.smith@weizmann.ac.il 4 University of California, Berkeley ARO Grant DAAD19-00-1-0177. #12;2 S. Chawla, C. Dwork, F. McSherry, A. Smith and H. Wee sanitization

Chawla, Shuchi

36

Building a Faculty Publications Database: A Case Study  

ERIC Educational Resources Information Center

This case study shares the experience of building an in-house faculty publications database that was spearheaded by the Touro College and University System library in 2010. The project began with the intention of contributing to the college by collecting the research accomplishments of our faculty and staff, thereby also increasing library…

Tabaei, Sara; Schaffer, Yitzchak; McMurray, Gregory; Simon, Bashe

2013-01-01

37

LEXITRAN for an easier public access to a patent database  

Microsoft Academic Search

This paper concerns work underway to improve public access to patent databases. It reports on the LEXITRAN project (LEXIcon TRANslation project).* This project is being carried out in collaboration between one of Europe's largest information vendors, QUESTEL, and two research laboratories from the CNRS and the Paris School of Mines. The goal of the project is three-fold: (1) apply natural

W. A. Turner; P. Buffet; F. Laville

1991-01-01

38

DATABASE LIKELIHOOD RATIOS AND FAMILIAL DNA KLAAS SLOOTEN AND RONALD MEESTER  

E-print Network

DATABASE LIKELIHOOD RATIOS AND FAMILIAL DNA SEARCHING KLAAS SLOOTEN AND RONALD MEESTER Abstract. Familial Searching is the process of searching in a DNA database for relatives of a given individual ratio, which is in this context called a Kinship Index. Suppose that the database contains, for a given

Meester, Ronald

39

A publication database for optical long baseline interferometry  

NASA Astrophysics Data System (ADS)

Optical long baseline interferometry is a technique that has generated almost 850 refereed papers to date. The targets span a large variety of objects from planetary systems to extragalactic studies and all branches of stellar physics. We have created a database hosted by the JMMC and connected to the Optical Long Baseline Interferometry Newsletter (OLBIN) web site using MySQL and a collection of XML or PHP scripts in order to store and classify these publications. Each entry is defined by its ADS bibcode, includes basic ADS informations and metadata. The metadata are specified by tags sorted in categories: interferometric facilities, instrumentation, wavelength of operation, spectral resolution, type of measurement, target type, and paper category, for example. The whole OLBIN publication list has been processed and we present how the database is organized and can be accessed. We use this tool to generate statistical plots of interest for the community in optical long baseline interferometry.

Malbet, Fabien; Mella, Guillaume; Lawson, Peter; Taillifet, Esther; Lafrasse, Sylvain

2010-07-01

40

Seattle Public Library Web Sites and Databases: Municipal Codes Online  

NSDL National Science Digital Library

Drawing heavily on the Folio databases made available by the Municipal Code Corporation, as well as other sources, Jeannette Voiland of the Seattle Public Library has compiled a growing list of over 150 municipal codes in 37 states at this time. Depth of coverage varies by state, with especially good coverage for Florida, California, and Washington. As the site grows, it should become a major repository for US municipal code information.

41

Dfam: a database of repetitive DNA based on profile hidden Markov models  

E-print Network

Dfam: a database of repetitive DNA based on profile hidden Markov models Travis J. Wheeler1 not been possible to apply profile HMM search to TE annotation because DNA search was too slow. However a database of repetitive DNA elements, called Dfam (http://dfam.janelia.org). Many genomes contain a large

Eddy, Sean

42

TRANSFAC: a database on transcription factors and their DNA binding sites.  

PubMed Central

TRANSFAC is a database about eukaryotic transcription regulating DNA sequence elements and the transcription factors binding to and acting through them. This report summarizes the present status of this database and accompanying retrieval tools. PMID:8594589

Wingender, E; Dietze, P; Karas, H; Knüppel, R

1996-01-01

43

RIDOM: Comprehensive and public sequence database for identification of Mycobacterium species  

PubMed Central

Background Molecular identification of Mycobacterium species has two primary advantages when compared to phenotypic identification: rapid turn-around time and improved accuracy. The information content of the 5' end of the 16S ribosomal RNA gene (16S rDNA) is sufficient for identification of most bacterial species. However, reliable sequence-based identification is hampered by many faulty and some missing sequence entries in publicly accessible databases. Methods In order to establish an improved 16S rDNA sequence database for the identification of clinical and environmental isolates, we sequenced both strands of the 5' end of 16S rDNA (Escherichia coli positions 54 to 510) from 199 mycobacterial culture collection isolates. All validly described species (n = 89; up to March 21, 2000) and nearly all published sequevar variants were included. If the 16S rDNA sequences were not discriminatory, the internal transcribed spacer (ITS) region sequences (n = 84) were also determined. Results Using 5'-16S rDNA sequencing a total of 64 different mycobacterial species (71.9%) could be identified. With the additional input of the ITS sequence, a further 16 species or subspecies could be differentiated. Only Mycobacterium tuberculosis complex species, M. marinum / M. ulcerans and the M. avium subspecies could not be differentiated using 5'-16S rDNA or ITS sequencing. A total of 77 culture collection strain sequences, exhibiting an overlap of at least 80% and identical by strain number to the isolates used in this study, were found in the GenBank. Comparing these with our sequences revealed that an average of 4.31 nucleotide differences (SD ± 0.57) were present. Conclusions The data from this analysis show that it is possible to differentiate most mycobacterial species by sequence analysis of partial 16S rDNA. The high-quality sequences reported here, together with ancillary information (e.g., taxonomic, medical), are available in a public database, which is currently being expanded in the RIDOM project ), for similarity searches. PMID:14611664

Harmsen, Dag; Dostal, Stefan; Roth, Andreas; Niemann, Stefan; Rothgänger, Jörg; Sammeth, Michael; Albert, Jürgen; Frosch, Matthias; Richter, Elvira

2003-01-01

44

75 FR 29155 - Publicly Available Consumer Product Safety Information Database  

Federal Register 2010, 2011, 2012, 2013, 2014

...Available Consumer Product Safety Information Database; Proposed Rule Federal Register / Vol...Available Consumer Product Safety Information Database AGENCY: Consumer Product Safety Commission...available consumer product safety information database (``database''). Section 212...

2010-05-24

45

75 FR 76831 - Publicly Available Consumer Product Safety Information Database  

Federal Register 2010, 2011, 2012, 2013, 2014

...Available Consumer Product Safety Information Database; Final Rule Federal Register / Vol...Available Consumer Product Safety Information Database AGENCY: Consumer Product Safety Commission...Available Consumer Product Safety Information Database (``Database''). Section 212...

2010-12-09

46

75 FR 41180 - Notice of Order: Revisions to Enterprise Public Use Database  

Federal Register 2010, 2011, 2012, 2013, 2014

...Revisions to Enterprise Public Use Database AGENCY: Federal Housing Finance Agency...responsibility to maintain a public use database (PUDB) for such mortgage data was transferred...purpose of loan data field in these two databases. 4. Single-family Data Field 27...

2010-07-15

47

Accessing the public MIMIC-II intensive care relational database for clinical research  

E-print Network

Background: The Multiparameter Intelligent Monitoring in Intensive Care II (MIMIC-II) database is a free, public resource for intensive care research. The database was officially released in 2006, and has attracted a growing ...

Scott, Daniel

48

High-throughput STR analysis for DNA database using direct PCR.  

PubMed

Since the Korean criminal DNA database was launched in 2010, we have focused on establishing an automated DNA database profiling system that analyzes short tandem repeat loci in a high-throughput and cost-effective manner. We established a DNA database profiling system without DNA purification using a direct PCR buffer system. The quality of direct PCR procedures was compared with that of conventional PCR system under their respective optimized conditions. The results revealed not only perfect concordance but also an excellent PCR success rate, good electropherogram quality, and an optimal intra/inter-loci peak height ratio. In particular, the proportion of DNA extraction required due to direct PCR failure could be minimized to <3%. In conclusion, the newly developed direct PCR system can be adopted for automated DNA database profiling systems to replace or supplement conventional PCR system in a time- and cost-saving manner. PMID:23683293

Sim, Jeong Eun; Park, Su Jeong; Lee, Han Chul; Kim, Se-Yong; Kim, Jong Yeol; Lee, Seung Hwan

2013-07-01

49

Evaluating DNA profile evidence when the suspect is identified through a database search  

Microsoft Academic Search

ABSTRACT: The paper is concerned with the strength of DNA evidence when a suspect is identified via a search through a database of the DNA profiles of known,individuals. Consideration of the appropriate likelihood ratio shows that in this setting the DNA evidence is (slightly) stronger than when,a suspect is identified by other means, subsequently profiled, and found to match. The

Dj Balding; P Donnelly

1996-01-01

50

Dfam: a Database of Repetitive DNA Based on Profile Hidden Markov Models  

E-print Network

1 Dfam: a Database of Repetitive DNA Based on Profile Hidden Markov Models Travis J. Wheeler. To date, it has not been possible to apply profile HMM search to TE annotation because DNA search was too brings the power of profile HMMs to DNA homology search with good speed (~10x slower than blastn

Eddy, Sean

51

Forensic DNA databases in Western Balkan region: retrospectives, perspectives, and initiatives  

PubMed Central

The European Network of Forensic Science Institutes (ENFSI) recommended the establishment of forensic DNA databases and specific implementation and management legislations for all EU/ENFSI members. Therefore, forensic institutions from Bosnia and Herzegovina, Serbia, Montenegro, and Macedonia launched a wide set of activities to support these recommendations. To assess the current state, a regional expert team completed detailed screening and investigation of the existing forensic DNA data repositories and associated legislation in these countries. The scope also included relevant concurrent projects and a wide spectrum of different activities in relation to forensics DNA use. The state of forensic DNA analysis was also determined in the neighboring Slovenia and Croatia, which already have functional national DNA databases. There is a need for a ‘regional supplement’ to the current documentation and standards pertaining to forensic application of DNA databases, which should include regional-specific preliminary aims and recommendations. PMID:21674821

Marjanovi?, Damir; Konjhodži?, Rijad; Butorac, Sara Sanela; Drobni?, Katja; Merkaš, Siniša; Lauc, Gordan; Primorac, Damir; An?elinovi?, Šimun; Milosavljevi?, Mladen; Karan, Željko; Vidovi?, Stojko; Stojkovi?, Oliver; Pani?, Bojana; Vu?eti? Dragovi?, An?elka; Kova?evi?, Sandra; Jakovski, Zlatko; Asplen, Chris; Primorac, Dragan

2011-01-01

52

[Current status of DNA databases in the forensic field: new progress, new legal needs].  

PubMed

One of the most polemic issues regarding the use of deoxyribonucleic acid (DNA) in the legal sphere, refers to the creation of DNA databases. Until relatively recently, Spain did not have a law to support the establishment of a national DNA profile bank for forensic purposes, and preserve the fundamental rights of subjects whose data are archived therein. The regulatory law of police databases regarding identifiers obtained from DNA approved in 2007, covers this void in the Spanish legislation and responds to the incessant need to adapt the laws to continuous scientific and technological progress. PMID:20476694

Baeta, Miriam; Martínez-Jarreta, Begoña

2009-01-01

53

UniPROBE: an online database of protein binding microarray data on protein–DNA interactions  

E-print Network

The UniPROBE (Universal PBM Resource for Oligonucleotide Binding Evaluation) database hosts data generated by universal protein binding microarray (PBM) technology on the in vitro DNA-binding specificities of proteins. ...

Bulyk, Martha L.

54

The EpiSLI Database: A Publicly Available Database on Speech and Language  

ERIC Educational Resources Information Center

Purpose: This article describes a database that was created in the process of conducting a large-scale epidemiologic study of specific language impairment (SLI). As such, this database will be referred to as the EpiSLI database. Children with SLI have unexpected and unexplained difficulties learning and using spoken language. Although there is no…

Tomblin, J. Bruce

2010-01-01

55

Databases and Bioinformatics Tools for the Study of DNA Repair  

PubMed Central

DNA is continuously exposed to many different damaging agents such as environmental chemicals, UV light, ionizing radiation, and reactive cellular metabolites. DNA lesions can result in different phenotypical consequences ranging from a number of diseases, including cancer, to cellular malfunction, cell death, or aging. To counteract the deleterious effects of DNA damage, cells have developed various repair systems, including biochemical pathways responsible for the removal of single-strand lesions such as base excision repair (BER) and nucleotide excision repair (NER) or specialized polymerases temporarily taking over lesion-arrested DNA polymerases during the S phase in translesion synthesis (TLS). There are also other mechanisms of DNA repair such as homologous recombination repair (HRR), nonhomologous end-joining repair (NHEJ), or DNA damage response system (DDR). This paper reviews bioinformatics resources specialized in disseminating information about DNA repair pathways, proteins involved in repair mechanisms, damaging agents, and DNA lesions. PMID:22091405

Milanowska, Kaja; Rother, Kristian; Bujnicki, Janusz M.

2011-01-01

56

DNA -- Intimate Information or Trash for Public Consumption?  

E-print Network

This essay discusses the increasingly popular police practice of covertly collecting DNA samples from people who inadvertently leave saliva, hair or other biological matter in public places. The essay contends that although the United States Supreme...

Wilson, Melanie D.

2008-01-01

57

The Moroccan Genetic Disease Database (MGDD): a database for DNA variations related to inherited disorders and disease susceptibility.  

PubMed

National and ethnic mutation databases provide comprehensive information about genetic variations reported in a population or an ethnic group. In this paper, we present the Moroccan Genetic Disease Database (MGDD), a catalogue of genetic data related to diseases identified in the Moroccan population. We used the PubMed, Web of Science and Google Scholar databases to identify available articles published until April 2013. The Database is designed and implemented on a three-tier model using Mysql relational database and the PHP programming language. To date, the database contains 425 mutations and 208 polymorphisms found in 301 genes and 259 diseases. Most Mendelian diseases in the Moroccan population follow autosomal recessive mode of inheritance (74.17%) and affect endocrine, nutritional and metabolic physiology. The MGDD database provides reference information for researchers, clinicians and health professionals through a user-friendly Web interface. Its content should be useful to improve researches in human molecular genetics, disease diagnoses and design of association studies. MGDD can be publicly accessed at http://mgdd.pasteur.ma. PMID:23860041

Charoute, Hicham; Nahili, Halima; Abidi, Omar; Gabi, Khalid; Rouba, Hassan; Fakiri, Malika; Barakat, Abdelhamid

2014-03-01

58

CD-ROM REVIEW: The ICRP Database of Dose Coefficients: Workers and Members of the Public  

Microsoft Academic Search

This CD contains the ICRP database of dose coefficients for workers and members of the public prepared by the DOCAL Task Group of ICRP Committee 2, and adopted by the Commission in October 1998. It is essentially an electronic version of ICRP Publications 68 and 72 for workers and members of the public, respectively. However, it contains far more data

Alan Bunker

1999-01-01

59

76 FR 53912 - FDA's Public Database of Products With Orphan-Drug Designation: Replacing Non-Informative Code...  

Federal Register 2010, 2011, 2012, 2013, 2014

...FDA-2011-N-0607] FDA's Public Database of Products With Orphan-Drug Designation...descriptive identifiers on its public database of products that have received orphan-drug...designation were published on our public database with non-informative code names....

2011-08-30

60

GBshape: a genome browser database for DNA shape annotations.  

PubMed

Many regulatory mechanisms require a high degree of specificity in protein-DNA binding. Nucleotide sequence does not provide an answer to the question of why a protein binds only to a small subset of the many putative binding sites in the genome that share the same core motif. Whereas higher-order effects, such as chromatin accessibility, cooperativity and cofactors, have been described, DNA shape recently gained attention as another feature that fine-tunes the DNA binding specificities of some transcription factor families. Our Genome Browser for DNA shape annotations (GBshape; freely available at http://rohslab.cmb.usc.edu/GBshape/) provides minor groove width, propeller twist, roll, helix twist and hydroxyl radical cleavage predictions for the entire genomes of 94 organisms. Additional genomes can easily be added using the GBshape framework. GBshape can be used to visualize DNA shape annotations qualitatively in a genome browser track format, and to download quantitative values of DNA shape features as a function of genomic position at nucleotide resolution. As biological applications, we illustrate the periodicity of DNA shape features that are present in nucleosome-occupied sequences from human, fly and worm, and we demonstrate structural similarities between transcription start sites in the genomes of four Drosophila species. PMID:25326329

Chiu, Tsu-Pei; Yang, Lin; Zhou, Tianyin; Main, Bradley J; Parker, Stephen C J; Nuzhdin, Sergey V; Tullius, Thomas D; Rohs, Remo

2015-01-28

61

Proposals to Regulate the Public's Rights to Use Information Stored in Databases  

NSDL National Science Digital Library

One of the items on the agenda for the 1996 World Intellectual Property Organization (WIPO) Diplomatic Conference (December 2-20 1996), is a database treaty that would effect the way databases are treated in terms of intellectual property. The proposed treaty "seeks to safeguard makers of databases against misappropriation of the fruits of their financial and professional investment in collecting, verifying and presenting the contents of databases. It does this by proposing protection that covers the whole or substantial parts of a database against certain acts by a user or by a competitor, for the limited duration of the right." Some have interpreted this to mean that the facts in the databases will become the intellectual property of the creators of the databases, a development that will have important consequences. Interested Internauts can decide for themselves by reading the treaty and a selection of responses that have been posted at public-domain.org.

1996-01-01

62

DNA banking and DNA databanking: Legal, ethical, and public policy issues  

SciTech Connect

The purpose of this research was to provide support to enable the authors to: (1) perform legal and empirical research and critically analyze DNA banking and DNA databanking as those activities are conducted by state forensic laboratories, the military, academic researchers, and commercial enterprises; and (2) develop a broadcast quality educational videotape for viewing by the general public about DNA technology and the privacy and related issues that it raises. The grant thus had both a research and analysis component and a public education component. This report outlines the work completed under the project.

Reilly, P.R.; McEwen, J.E.; Lawyer, J.D.; Small, D.

1997-04-30

63

76 FR 60031 - Notice of Order: Revisions to Enterprise Public Use Database Incorporating High-Cost Single...  

Federal Register 2010, 2011, 2012, 2013, 2014

...Revisions to Enterprise Public Use Database Incorporating High-Cost Single-Family...single-family matrix in FHFA's Public Use Database (PUDB) to include data fields for the...variety of loan attributes in FHFA's databases that could be used, singularly or...

2011-09-28

64

An assessment of whether SNPs will replace STRs in national DNA databases Joint considerations of the  

E-print Network

of the DNA working group of the European Network of Forensic Science Institutes (ENFSI) and the Scientific as the preferred method of testing of forensic samples and database samples in the near to medium future and is not directly applicable to forensic use. This is because forensic scientists have to contend with small

65

An Internet-Accessible DNA Sequence Database for Identifying Fusaria from Human and Animal Infections  

Technology Transfer Automated Retrieval System (TEKTRAN)

Because less than one-third of clinically relevant fusaria can be accurately identified to species level using phenotypic data (i.e., morphological species recognition), we constructed a three-locus DNA sequence database to facilitate molecular identification of the 69 Fusarium species associated wi...

66

Codon usage tabulated from international DNA sequence databases: status for the year 2000  

Microsoft Academic Search

The frequencies of each of the 257 468 complete protein coding sequences (CDSs) have been compiled from the taxonomical divisions of the GenBank DNA sequence database. The sum of the codons used by 8792 organisms has also been calculated. The data files can be obtained from the anonymous ftp sites of DDBJ, Kazusa and EBI. A list of the codon

Yasukazu Nakamura; Takashi Gojobori; Toshimichi Ikemura

2000-01-01

67

Literature curation of protein interactions: measuring agreement across major public databases  

PubMed Central

Literature curation of protein interaction data faces a number of challenges. Although curators increasingly adhere to standard data representations, the data that various databases actually record from the same published information may differ significantly. Some of the reasons underlying these differences are well known, but their global impact on the interactions collectively curated by major public databases has not been evaluated. Here we quantify the agreement between curated interactions from 15?471 publications shared across nine major public databases. Results show that on average, two databases fully agree on 42% of the interactions and 62% of the proteins curated from the same publication. Furthermore, a sizable fraction of the measured differences can be attributed to divergent assignments of organism or splice isoforms, different organism focus and alternative representations of multi-protein complexes. Our findings highlight the impact of divergent curation policies across databases, and should be relevant to both curators and data consumers interested in analyzing protein-interaction data generated by the scientific community. Database URL: http://wodaklab.org/iRefWeb PMID:21183497

Turinsky, Andrei L.; Razick, Sabry; Turner, Brian; Wodak, Shoshana J.

2010-01-01

68

Complementarity between public and commercial databases: new opportunities in medicinal chemistry informatics  

Microsoft Academic Search

The last two years have seen a dramatic expansion in public cheminformatics, as exemplified by the approximate five-fold growth of PubChem from over 50 contributing data sources. Consequently, medicinal chemists who were hitherto limited to commercial databases now also have access to public sources that they can download and\\/or query directly over the Web. The range of public sources, particularly

Christopher Southan; P'eter V'arkonyi; Sorel Muresan

2007-01-01

69

Bioethical Biobanks: Three Concerns in Designing and Using Law Enforcement DNA Identification Databases  

SciTech Connect

Federal and state law enforcement authorities have amassed large collections of DNA samples and the identifying profiles derived from them. These databases help to identify the guilty and to exonerate the innocent, but as the databanks grow, so do fears about civil liberties. The research reported here discusses three legal and social policy issues that have been raised in regard to these biobanks—the choice of loci to type for identifying individuals, the indefinite retention of DNA samples, and the use of the DNA samples or the identifying profiles for research purposes. It also considers the possible value of the databases for research into the genetics of human behavior and the ethics of using them for this purpose. It rejects the broad claim that such research is inherently unethical but proposes procedures for ensuring that the value of the proposed research justifies any psychosocial or other risks to the subjects of the research.

D.H. Kaye

2006-10-19

70

The annotation and the usage of scientific databases could be improved with public issue tracker software  

PubMed Central

Since the publication of their longtime predecessor The Atlas of Protein Sequences and Structures in 1965 by Margaret Dayhoff, scientific databases have become a key factor in the organization of modern science. All the information and knowledge described in the novel scientific literature is translated into entries in many different scientific databases, making it possible to obtain very accurate information on a biological entity like genes or proteins without having to manually review the literature on it. However, even for the databases with the finest annotation procedures, errors or unclear parts sometimes appear in the publicly released version and influence the research of unaware scientists using them. The researcher that finds an error in a database is often left in a uncertain state, and often abandons the effort of reporting it because of a lack of a standard procedure to do so. In the present work, we propose that the simple adoption of a public error tracker application, as in many open software projects, could improve the quality of the annotations in many databases and encourage feedback from the scientific community on the data annotated publicly. In order to illustrate the situation, we describe a series of errors that we found and helped solve on the genes of a very well-known pathway in various biomedically relevant databases. We would like to show that, even if a majority of the most important scientific databases have procedures for reporting errors, these are usually not publicly visible, making the process of reporting errors time consuming and not useful. Also, the effort made by the user that reports the error often goes unacknowledged, putting him in a discouraging position. PMID:21186182

Dall'Olio, Giovanni Marco; Bertranpetit, Jaume; Laayouni, Hafid

2010-01-01

71

MethylomeDB: a database of DNA methylation profiles of the brain  

PubMed Central

MethylomeDB (http://epigenomics.columbia.edu/methylomedb/index.html) is a new database containing genome-wide brain DNA methylation profiles. DNA methylation is an important epigenetic mark in the mammalian brain. In human studies, aberrant DNA methylation alterations have been associated with various neurodevelopmental and neuropsychiatric disorders such as schizophrenia, and depression. In this database, we present methylation profiles of carefully selected non-psychiatric control, schizophrenia, and depression samples. We also include data on one mouse forebrain sample specimen to allow for cross-species comparisons. In addition to our DNA methylation data generated in-house, we have and will continue to include published DNA methylation data from other research groups with the focus on brain development and function. Users can view the methylation data at single-CpG resolution with the option of wiggle and microarray formats. They can also download methylation data for individual samples. MethylomeDB offers an important resource for research into brain function and behavior. It provides the first source of comprehensive brain methylome data, encompassing whole-genome DNA methylation profiles of human and mouse brain specimens that facilitate cross-species comparative epigenomic investigations, as well as investigations of schizophrenia and depression methylomes. PMID:22140101

Xin, Yurong; Chanrion, Benjamin; O'Donnell, Anne H.; Milekic, Maria; Costa, Ramiro; Ge, Yongchao; Haghighi, Fatemeh G.

2012-01-01

72

Development of a 20-locus fluorescent multiplex system as a valuable tool for national DNA database.  

PubMed

The multiplex system allows the detection of 19 autosomal short tandem repeat (STR) loci [including all Combined DNA Index System (CODIS) STR loci as well as D2S1338, D6S1043, D12S391, D19S433, Penta D and Penta E] plus the sex-determining locus Amelogenin in a single reaction, comprising all STR loci in various commercial kits used in the China national DNA database (NDNAD). Primers are designed so that the amplicons are distributed ranging from 90 base pairs (bp) to 450 bp within a five-dye fluorescent design with the fifth dye reserved for the internal size standard. With 30 cycles, 125 pg to 2 ng DNA template showed optimal profiling result, while robust profiles could also be achieved by adjusting the cycle numbers for the DNA template beyond that optimal DNA input range. Mixture studies showed that 83% and 87% of minor alleles were detected at 9:1 and 1:9 ratios, respectively. When 4 ng of degraded DNA was digested by 2-min DNase and 1 ng undegraded DNA was added to 400 ?M haematin, the complete profiles were still observed. Polymerase chain reaction (PCR)-based procedures were examined and optimized including the concentrations of primer set, magnesium and the Taq polymerase as well as volume, cycle number and annealing temperature. In addition, the system has been validated by 3000 bloodstain samples and 35 common case samples in line with the Chinese National Standards and Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. The total probability of identity (TPI) can reach to 8×10(-24), where DNA database can be improved at the level of 10 million DNA profiles or more because the number of expected match is far from one person (4×10(-10)) and can be negligible. Further, our system also demonstrates its good performance in case samples and it will be an ideal tool for forensic DNA typing and databasing with potential application. PMID:23266302

Jiang, Xianhua; Guo, Fei; Jia, Fei; Jin, Ping; Sun, Zhu

2013-02-01

73

Bioinformatic databases and resources in the public domain to aid HLA research.  

PubMed

Research in HLA as in any other field depends on information. Different groups have generated generic and specific resources and tools to support this research. The present review describes a qualified subset of these resources, which should cover the most important starting points for research in the HLA field. It discusses access to HLA allele sequences, allele frequencies, continues with general support to access to literature, DNA and protein sequence information, structural models, teaching books, databases with phenotypic datasets, alignment tools, peptide binding, statistical tools, guidelines and ambiguity coding. Following functionalities and databases have been included: IMGT/HLA, Immuno Polymorphism Database (IPD), allele frequencies*.net, a detailed look into NCBI (National Center of Biotechnology Information) with a subset of databases and tools, focusing on literature research, sequences, user-specific support tools and applications (PubMed, GenBank, MyNCBI, blast, Gene, MapViewer, Structure, CN3D, WorkBench, and dbMHC). This is followed by a brief survey of EBI-EMBL/Ensemble, the sequence alignment tool Clustal, the peptide and ligand databases SYFPEITHI and Immune Epitope Database, and last but not least statistical packages and HLA allele coding resources PyPop, the Immuno-genomics Data Analysis Working Group and the NMDP informatics section. All databases and tools can be freely accessed. Data linked to individuals, however, might require authorization by a data access committee. PMID:22994154

Helmberg, W

2012-10-01

74

Looking for Cancer Clues in Publicly Accessible Databases  

PubMed Central

What started out as a mere attempt to tentatively identify proteins in experimental cancer-related 2D-PAGE maps developed into VIRTUAL2D, a web-accessible repository for theoretical pI/MW charts for 92 organisms. Using publicly available expression data, we developed a collection of tissue-specific plots based on differential gene expression between normal and diseased states. We use this comparative cancer proteomics knowledge base, known as the tissue molecular anatomy project (TMAP), to uncover threads of cancer markers common to several types of cancer and to relate this information to established biological pathways. PMID:18629065

Lemkin, Peter F.; Smythers, Gary W.; Munroe, David J.

2004-01-01

75

The 2008 Public Release of the International Multi-tokamak Confinement Profile Database  

SciTech Connect

This paper documents the public release PR08 of the International Tokamak Physics Activity (ITPA) profile database, which should be of particular interest to the magnetic confinement fusion community. Data from a wide variety of interesting discharges from many of the world's leading tokamak experiments are now made available in PR08, which also includes predictive simulations of an initial set of operating scenarios for ITER. In this paper we describe the discharges that have been included and the tools that are available to the reader who is interested in accessing and working with the data. Most discharge descriptions refer to more detailed previous publications. In addition, we review physics analyses that have already made use of the profile database discharges. Public access to PR08 data is unconditional, but this paper should be cited by any publication that makes use of PR08 data.

Roach, C M [UKAEA Fusion, Culham UK; Walters, M [UKAEA Fusion, Culham UK; Budny, R. V. [Princeton Plasma Physics Laboratory (PPPL); Murakami, Masanori [ORNL

2008-01-01

76

"Would you accept having your DNA profile inserted in the National Forensic DNA database? Why?" Results of a questionnaire applied in Portugal.  

PubMed

The creation and expansion of forensic DNA databases might involve potential threats to the protection of a range of human rights. At the same time, such databases have social benefits. Based on data collected through an online questionnaire applied to 628 individuals in Portugal, this paper aims to analyze the citizens' willingness to donate voluntarily a sample for profiling and inclusion in the National Forensic DNA Database and the views underpinning such a decision. Nearly one-quarter of the respondents would indicate 'no', and this negative response increased significantly with age and education. The overriding willingness to accept the inclusion of the individual genetic profile indicates an acknowledgement of the investigative potential of forensic DNA technologies and a relegation of civil liberties and human rights to the background, owing to the perceived benefits of protecting both society and the individual from crime. This rationale is mostly expressed by the idea that all citizens should contribute to the expansion of the National Forensic DNA Database for reasons that range from the more abstract assumption that donating a sample for profiling would be helpful in fighting crime to the more concrete suggestion that everyone (criminals and non-criminals) should be in the database. The concerns with the risks of accepting the donation of a sample for genetic profiling and inclusion in the National Forensic DNA Database are mostly related to lack of control and insufficient or unclear regulations concerning safeguarding individuals' data and supervising the access and uses of genetic data. By providing an empirically-grounded understanding of the attitudes regarding willingness to donate voluntary a sample for profiling and inclusion in a National Forensic DNA Database, this study also considers the citizens' perceived benefits and risks of operating forensic DNA databases. These collective views might be useful for the formation of international common ethical standards for the development and governance of DNA databases in a framework in which the citizens' perspectives are taken into consideration. PMID:24315600

Machado, Helena; Silva, Susana

2014-01-01

77

Development and Evaluation of a Quality-Controlled Ribosomal Sequence Database for 16S Ribosomal DNA-Based Identification of Staphylococcus Species  

PubMed Central

To establish an improved ribosomal gene sequence database as part of the Ribosomal Differentiation of Microorganisms (RIDOM) project and to overcome the drawbacks of phenotypic identification systems and publicly accessible sequence databases, both strands of the 5? end of the 16S ribosomal DNA (rDNA) of 81 type and reference strains comprising all validly described staphylococcal (sub)species were sequenced. Assuming a normal distribution for pairwise distances of all unique staphylococcal sequences and choosing a reporting criterion of ?98.7% similarity for a “distinct species,” a statistical error probability of 1.0% was calculated. To evaluate this database, a 16S rDNA fragment (corresponding to Escherichia coli positions 54 to 510) of 55 clinical Staphylococcus isolates (including those of the small-colony variant phenotype) were sequenced and analyzed by the RIDOM approach. Of these isolates, 54 (98.2%) had a similarity score above the proposed threshold using RIDOM; 48 (87.3%) of the sequences gave a perfect match, whereas 83.6% were found by searching National Center for Biotechnology Information (NCBI) database entries. In contrast to RIDOM, which showed four ambiguities at the species level (mainly concerning Staphylococcus intermedius versus Staphylococcus delphini), the NCBI database search yielded 18 taxon-related ambiguities and showed numerous matches exhibiting redundant or unspecified entries. Comparing molecular results with those of biochemical procedures, ID 32 Staph (bioMérieux, Marcy I'Etoile, France) and VITEK 2 (bioMérieux) failed to identify 13 (23.6%) and 19 (34.5%) isolates, respectively, due to incorrect identification and/or categorization below acceptable values. In contrast to phenotypic methods and the NCBI database, the novel high-quality RIDOM sequence database provides excellent identification of staphylococci, including rarely isolated species and phenotypic variants. PMID:15528685

Becker, Karsten; Harmsen, Dag; Mellmann, Alexander; Meier, Christian; Schumann, Peter; Peters, Georg; von Eiff, Christof

2004-01-01

78

Towards a public analysis database for LHC new physics searches using MadAnalysis 5  

E-print Network

We present the implementation, in the MadAnalysis 5 framework, of several ATLAS and CMS searches for supersymmetry in data recorded during the first run of the LHC. We provide extensive details on the validation of our implementations and propose to create a public analysis database within this framework.

B. Dumont; B. Fuks; S. Kraml; S. Bein; G. Chalons; E. Conte; S. Kulkarni; D. Sengupta; C. Wymant

2015-01-27

79

Governing Software: Networks, Databases and Algorithmic Power in the Digital Governance of Public Education  

ERIC Educational Resources Information Center

This article examines the emergence of "digital governance" in public education in England. Drawing on and combining concepts from software studies, policy and political studies, it identifies some specific approaches to digital governance facilitated by network-based communications and database-driven information processing software…

Williamson, Ben

2015-01-01

80

IRB and EDRC Release New Policy Governing Public Databases Date: February 22, 2013  

E-print Network

involving secondary analysis of publicly available databases. "This policy reduces the burden on MCW available including: American College of Surgeons National Trauma Data Bank (NTDB), and several Kirsten Beyer. The EDRC is MCW's centralized source for secondary health and demographic data

81

DNA Identification of Mountain Lions Involved in Livestock Predation and Public Safety Incidents and Investigations  

E-print Network

1 DNA Identification of Mountain Lions Involved in Livestock Predation and Public Safety Incidents concolor, bobcat, forensic, genetics, DNA techniques, noninvasive sampling, fecal DNA, prey swab DNA ABSTRACT Using three case studies, we demonstrated the utility of techniques to analyze DNA from trace

Ernest, Holly

82

76 FR 77533 - Notice of Order: Revisions to Enterprise Public Use Database Incorporating High-Cost Single...  

Federal Register 2010, 2011, 2012, 2013, 2014

...2011-N-13] Notice of Order: Revisions to Enterprise Public Use Database Incorporating High-Cost Single-Family Securitized Loan...FHFA's adoption of an Order revising FHFA's Public Use Database matrices to include certain data fields for high-cost...

2011-12-13

83

A comparison of adjustment methods to test the robustness of an STR DNA database comprised of 24 European populations  

Microsoft Academic Search

An aim of the European Network of Forensic Science Institutes (ENFSI) is to produce a DNA database of second generation multiplex (SGM) STR profiles that is representative of the resident cosmopolitan populations. To achieve this, data were collected from 24 different populations. All of the data were combined to form one database of 5700 profiles from which allele proportions were

Peter Gill; Lindsey Foreman; John S Buckleton; Christopher M Triggs; Heather Allen

2003-01-01

84

Genomics and Public Health Research: Can the State Allow Access to Genomic Databases?  

PubMed Central

Because many diseases are multifactorial disorders, the scientific progress in genomics and genetics should be taken into consideration in public health research. In this context, genomic databases will constitute an important source of information. Consequently, it is important to identify and characterize the State’s role and authority on matters related to public health, in order to verify whether it has access to such databases while engaging in public health genomic research. We first consider the evolution of the concept of public health, as well as its core functions, using a comparative approach (e.g. WHO, PAHO, CDC and the Canadian province of Quebec). Following an analysis of relevant Quebec legislation, the precautionary principle is examined as a possible avenue to justify State access to and use of genomic databases for research purposes. Finally, we consider the Influenza pandemic plans developed by WHO, Canada, and Quebec, as examples of key tools framing public health decision-making process. We observed that State powers in public health, are not, in Quebec, well adapted to the expansion of genomics research. We propose that the scope of the concept of research in public health should be clear and include the following characteristics: a commitment to the health and well-being of the population and to their determinants; the inclusion of both applied research and basic research; and, an appropriate model of governance (authorization, follow-up, consent, etc.). We also suggest that the strategic approach version of the precautionary principle could guide collective choices in these matters. PMID:23113174

Cousineau, J; Girard, N; Monardes, C; Leroux, T; Jean, M Stanton

2012-01-01

85

Feline Non-repetitive Mitochondrial DNA Control Region Database for Forensic Evidence  

PubMed Central

The domestic cat is the one of the most popular pets throughout the world. A by-product of owning, interacting with, or being in a household with a cat is the transfer of shed fur to clothing or personal objects. As trace evidence, transferred cat fur is a relatively untapped resource for forensic scientists. Both phenotypic and genotypic characteristics can be obtained from cat fur, but databases for neither aspect exist. Because cats incessantly groom, cat fur may have nucleated cells, not only in the hair bulb, but also as epithelial cells on the hair shaft deposited during the grooming process, thereby generally providing material for DNA profiling. To effectively exploit cat hair as a resource, representative databases must be established. This study evaluates 402 bp of the mtDNA control region (CR) from 1,394 cats, including cats from 25 distinct worldwide populations and 26 breeds. Eighty-three percent of the cats are represented by 12 major mitotypes. An additional 8.0% are clearly derived from the major mitotypes. Unique sequences were found in 7.5% of the cats. The overall genetic diversity for this data set was 0.8813 ± 0.0046 with a random match probability of 11.8%. This region of the cat mtDNA has discriminatory power suitable for forensic application worldwide. PMID:20457082

Grahn, R. A.; Kurushima, J. D.; Billings, N. C.; Grahn, J.C.; Halverson, J. L.; Hammer, E.; Ho, C.K.; Kun, T. J.; Levy, J.K.; Lipinski, M. J.; Mwenda, J.M.; Ozpinar, H.; Schuster, R.K; Shoorijeh, S.J.; Tarditi, C. R.; Waly, N.E.; Wictum, E. J.; Lyons, L. A.

2010-01-01

86

Government databases and public health research: facilitating access in the public interest.  

PubMed

Access to datasets of personal health information held by government agencies is essential to support public health research and to promote evidence-based public health policy development. Privacy legislation in Australia allows the use and disclosure of such information for public health research. However, access is not always forthcoming in a timely manner and the decision-making process undertaken by government data custodians is not always transparent. Given the public benefit in research using these health information datasets, this article suggests that it is time to recognise a right of access for approved research and that the decisions, and decision-making processes, of government data custodians should be subject to increased scrutiny. The article concludes that researchers should have an avenue of external review where access to information has been denied or unduly delayed. PMID:25087372

Adams, Carolyn; Allen, Judy

2014-06-01

87

REBASE-a database for DNA restriction and modification: enzymes, genes and genomes.  

PubMed

REBASE is a comprehensive and fully curated database of information about the components of restriction-modification (RM) systems. It contains fully referenced information about recognition and cleavage sites for both restriction enzymes and methyltransferases as well as commercial availability, methylation sensitivity, crystal and sequence data. All genomes that are completely sequenced are analyzed for RM system components, and with the advent of PacBio sequencing, the recognition sequences of DNA methyltransferases (MTases) are appearing rapidly. Thus, Type I and Type III systems can now be characterized in terms of recognition specificity merely by DNA sequencing. The contents of REBASE may be browsed from the web http://rebase.neb.com and selected compilations can be downloaded by FTP (ftp.neb.com). Monthly updates are also available via email. PMID:25378308

Roberts, Richard J; Vincze, Tamas; Posfai, Janos; Macelis, Dana

2015-01-28

88

Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes  

PubMed Central

Although the capability of DNA to form a variety of non-canonical (non-B) structures has long been recognized, the overall significance of these alternate conformations in biology has only recently become accepted en masse. In order to provide access to genome-wide locations of these classes of predicted structures, we have developed non-B DB, a database integrating annotations and analysis of non-B DNA-forming sequence motifs. The database provides the most complete list of alternative DNA structure predictions available, including Z-DNA motifs, quadruplex-forming motifs, inverted repeats, mirror repeats and direct repeats and their associated subsets of cruciforms, triplex and slipped structures, respectively. The database also contains motifs predicted to form static DNA bends, short tandem repeats and homo(purine•pyrimidine) tracts that have been associated with disease. The database has been built using the latest releases of the human, chimp, dog, macaque and mouse genomes, so that the results can be compared directly with other data sources. In order to make the data interpretable in a genomic context, features such as genes, single-nucleotide polymorphisms and repetitive elements (SINE, LINE, etc.) have also been incorporated. The database is accessed through query pages that produce results with links to the UCSC browser and a GBrowse-based genomic viewer. It is freely accessible at http://nonb.abcc.ncifcrf.gov. PMID:21097885

Cer, Regina Z.; Bruce, Kevin H.; Mudunuri, Uma S.; Yi, Ming; Volfovsky, Natalia; Luke, Brian T.; Bacolla, Albino; Collins, Jack R.; Stephens, Robert M.

2011-01-01

89

Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes.  

PubMed

Although the capability of DNA to form a variety of non-canonical (non-B) structures has long been recognized, the overall significance of these alternate conformations in biology has only recently become accepted en masse. In order to provide access to genome-wide locations of these classes of predicted structures, we have developed non-B DB, a database integrating annotations and analysis of non-B DNA-forming sequence motifs. The database provides the most complete list of alternative DNA structure predictions available, including Z-DNA motifs, quadruplex-forming motifs, inverted repeats, mirror repeats and direct repeats and their associated subsets of cruciforms, triplex and slipped structures, respectively. The database also contains motifs predicted to form static DNA bends, short tandem repeats and homo(purine•pyrimidine) tracts that have been associated with disease. The database has been built using the latest releases of the human, chimp, dog, macaque and mouse genomes, so that the results can be compared directly with other data sources. In order to make the data interpretable in a genomic context, features such as genes, single-nucleotide polymorphisms and repetitive elements (SINE, LINE, etc.) have also been incorporated. The database is accessed through query pages that produce results with links to the UCSC browser and a GBrowse-based genomic viewer. It is freely accessible at http://nonb.abcc.ncifcrf.gov. PMID:21097885

Cer, Regina Z; Bruce, Kevin H; Mudunuri, Uma S; Yi, Ming; Volfovsky, Natalia; Luke, Brian T; Bacolla, Albino; Collins, Jack R; Stephens, Robert M

2011-01-01

90

Effect of reference database on frequency estimates of polymerase chain reaction (PCR)-based DNA profiles.  

PubMed

A variety of general, regional, ancestral and ethnic databases is available for the polymerase chain reaction (PCR)-based loci LDLR, GYPA, HBGG, D7S8, Gc, DQA1, and D1S80. Generally, we observed greater differences in frequency estimations of DNA profiles between racial groups than between ethnic or geographic subgroups. Analysis revealed few forensically significant differences within ethnic subgroups, particularly within general United States groups, and multi-locus frequency estimates typically differ by less than a factor of ten. Using a database different from the one to which a target profile belongs tends to overestimate rarity. Implementation of the general correction of homozygote frequencies for a population substructure, advised by the 1996 National Research Council report, The Evaluation of Forensic DNA Evidence, has a minimal effect on profile frequencies. Even when it is known that both the suspect and all possible perpetrators must belong to the same isolated population, the special correction for inbreeding, which was proposed by the 1996 National Research Council report for this special case, has a relatively modest effect, typically a factor of two or less for 1% inbreeding. The effect becomes more substantial (exceeding a factor of ten) for inbreeding of 3% or more in multi-locus profiles rarer than about one in a million. PMID:9608687

Monson, K L; Budowle, B

1998-05-01

91

Accelerating ultrasound image analysis research through publically available database Vikas Revanna Shivaprabhu, Andinet Enquobahrie, Zach Mullen, Stephen Aylward  

E-print Network

with lung lesions marked by up to four radiologists [LIDC]. Image archive of CT lung cancer patients is made of the recorded US image. 2. METHOD To generate publicly available database, we used a TeleMed Ultrasound System

Stetten, George

92

The public sequencing process, John SulstonSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

Interviewee: John Sulston DNAi Location:Genome>The project>players>Public The public sequencing process Nobel Laureate John Sulston, a key figure in the UK sequencing effort, talks about breaking DNA apart so that the sequence can be reassembled.

2008-10-06

93

dndDB: A Database Focused on Phosphorothioation of the DNA Backbone  

PubMed Central

Background The Dnd DNA degradation phenotype was first observed during electrophoresis of genomic DNA from Streptomyces lividans more than 20 years ago. It was subsequently shown to be governed by the five-gene dnd cluster. Similar gene clusters have now been found to be widespread among many other distantly related bacteria. Recently the dnd cluster was shown to mediate the incorporation of sulphur into the DNA backbone via a sequence-selective, stereo-specific phosphorothioate modification in Escherichia coli B7A. Intriguingly, to date all identified dnd clusters lie within mobile genetic elements, the vast majority in laterally transferred genomic islands. Methodology We organized available data from experimental and bioinformatics analyses about the DNA phosphorothioation phenomenon and associated documentation as a dndDB database. It contains the following detailed information: (i) Dnd phenotype; (ii) dnd gene clusters; (iii) genomic islands harbouring dnd genes; (iv) Dnd proteins and conserved domains. As of 25 December 2008, dndDB contained data corresponding to 24 bacterial species exhibiting the Dnd phenotype reported in the scientific literature. In addition, via in silico analysis, dndDB identified 26 syntenic dnd clusters from 25 species of Eubacteria and Archaea, 25 dnd-bearing genomic islands and one dnd plasmid containing 114 dnd genes. A further 397 other genes coding for proteins with varying levels of similarity to Dnd proteins were also included in dndDB. A broad range of similarity search, sequence alignment and phylogenetic tools are readily accessible to allow for to individualized directions of research focused on dnd genes. Conclusion dndDB can facilitate efficient investigation of a wide range of aspects relating to dnd DNA modification and other island-encoded functions in host organisms. dndDB version 1.0 is freely available at http://mml.sjtu.edu.cn/dndDB/. PMID:19357771

Ou, Hong-Yu; He, Xinyi; Shao, Yucheng; Tai, Cui; Rajakumar, Kumar; Deng, Zixin

2009-01-01

94

DNA perfume and improving public knowledge, Francis CollinsSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

Interviewee: Francis Collins DNAi Location:Timeline>1990s I arrived here April the 4th, 1993, an auspicious day because that very day I, as I opened the newspaper I realized that that was probably going to be remembered in the annals of DNA, not because of me, because that didn't seem like that was going to be so significant, but because that was the day that DNA perfume was issued, all kinds of advertising all over the place about, go out and buy this perfume. And it was a bit jarring because the perfume bottle was in the shape of a helix but it was actually a triple helix, making it very clear we had an educational challenge as well as a scientific challenge if this project was ever going to achieve the public benefit that we all hoped for.

2008-03-26

95

Public Perceptions and Expectations of the Forensic Use of DNA: Results of a Preliminary Study  

ERIC Educational Resources Information Center

The forensic use of Deoxyribonucleic Acid (DNA) is demonstrating significant success as a crime-solving tool. However, numerous concerns have been raised regarding the potential for DNA use to contravene cultural, ethical, and legal codes. In this article the expectations and level of knowledge of the New Zealand public of the DNA data-bank and…

Curtis, Cate

2009-01-01

96

Reusable data in public health data-bases-problems encountered in Danish Children's Database.  

PubMed

Denmark have unique health informatics databases e.g. "The Children's Database", which since 2009 holds data on all Danish children from birth until 17 years of age. In the current set-up a number of potential sources of errors exist - both technical and human-which means that the data is flawed. This gives rise to erroneous statistics and makes the data unsuitable for research purposes. In order to make the data usable, it is necessary to develop new methods for validating the data generation process at the municipal/regional/national level. In the present ongoing research project, two research areas are combined: Public Health Informatics and Computer Science, and both ethnographic as well as system engineering research methods are used. The project is expected to generate new generic methods and knowledge about electronic data collection and transmission in different social contexts and by different social groups and thus to be of international importance, since this is sparsely documented in the Public Health Informatics perspective. This paper presents the preliminary results, which indicate that health information technology used ought to be subject for redesign, where a thorough insight into the work practices should be point of departure. PMID:22874263

Høstgaard, Anna Marie; Pape-Haugaard, Louise

2012-01-01

97

First whole genome based microsatellite DNA marker database of tomato for mapping and variety identification  

PubMed Central

Background The cultivated tomato is second most consumed vegetable of the world and is an important part of a diverse and balanced diet as a rich source of vitamins, minerals, phenolic antioxidants and antioxidant lycopene having anti-cancer properties. To reap benefit of genomics of the domestic tomato (Solanum lycopersicum L.) unravelled by Tomato Genome Consortium (The Tomato Genome Consortium, 2012), the bulk mining of its markers in totality is imperative and critically required. The solgenomics has limited number of microsatellite DNA markers (2867) pertaining to solanaceae family. As these markers are of linkage map having relative distance, the choice of selected markers based on absolute distance as of physical map is missing. Only limited microsatellite markers with limitations are reported for variety identification thus there is a need for more markers supplementing DUS test and also for traceability of product in global market. Description We present here the first whole genome based microsatellite DNA marker database of tomato, TomSatDB (Tomato MicroSatellite Database) with more than 1.4 million markers mined in-silico, using MIcroSAtellite (MISA) tool. To cater the customized needs of wet lab, features with a novelty of an automated primer designing tool is added. TomSatDB (http://cabindb.iasri.res.in/tomsatdb), a user-friendly and freely accessible tool offers chromosome wise as well as location wise search of primers. It is an online relational database based on “three-tier architecture” that catalogues information of microsatellites in MySQL and user-friendly interface developed using PHP (Hypertext Pre Processor). Conclusion Besides abiotic stress, tomato is known to have biotic stress due to its susceptibility over 200 diseases caused by pathogenic fungi, bacteria, viruses and nematodes. These markers are expected to pave the way of germplasm management over abiotic and biotic stress as well as improvement through molecular breeding, leading to increased tomato productivity in India as well as other parts of the world. In era of IPR the new variety can be identified based on allelic variation among varieties supplementing DUS test and product traceability.

2013-01-01

98

Dfam: a database of repetitive DNA based on profile hidden Markov models  

PubMed Central

We present a database of repetitive DNA elements, called Dfam (http://dfam.janelia.org). Many genomes contain a large fraction of repetitive DNA, much of which is made up of remnants of transposable elements (TEs). Accurate annotation of TEs enables research into their biology and can shed light on the evolutionary processes that shape genomes. Identification and masking of TEs can also greatly simplify many downstream genome annotation and sequence analysis tasks. The commonly used TE annotation tools RepeatMasker and Censor depend on sequence homology search tools such as cross_match and BLAST variants, as well as Repbase, a collection of known TE families each represented by a single consensus sequence. Dfam contains entries corresponding to all Repbase TE entries for which instances have been found in the human genome. Each Dfam entry is represented by a profile hidden Markov model, built from alignments generated using RepeatMasker and Repbase. When used in conjunction with the hidden Markov model search tool nhmmer, Dfam produces a 2.9% increase in coverage over consensus sequence search methods on a large human benchmark, while maintaining low false discovery rates, and coverage of the full human genome is 54.5%. The website provides a collection of tools and data views to support improved TE curation and annotation efforts. Dfam is also available for download in flat file format or in the form of MySQL table dumps. PMID:23203985

Wheeler, Travis J.; Clements, Jody; Eddy, Sean R.; Hubley, Robert; Jones, Thomas A.; Jurka, Jerzy; Smit, Arian F. A.; Finn, Robert D.

2013-01-01

99

Similarity landscapes: An improved method for scientific visualization of information from protein and DNA database searches  

SciTech Connect

This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The authors have used computer simulations and examination of a variety of databases to answer questions about a wide range of evolutionary questions. The authors have found that there is a clear distinction in the evolution of HIV-1 and HIV-2, with the former and more virulent virus evolving more rapidly at a functional level. The authors have discovered highly non-random patterns in the evolution of HIV-1 that can be attributed to a variety of selective pressures. In the course of examination of microsatellite DNA (short repeat regions) in microorganisms, the authors have found clear differences between prokaryotes and eukaryotes in their distribution, differences that can be tied to different selective pressures. They have developed a new method (topiary pruning) for enhancing the phylogenetic information contained in DNA sequences. Most recently, the authors have discovered effects in complex rainforest ecosystems that indicate strong frequency-dependent interactions between host species and their parasites, leading to the maintenance of ecosystem variability.

Dogget, N.; Myers, G. [Los Alamos National Lab., NM (United States); Wills, C.J. [Univ. of California, San Diego, CA (United States)

1998-12-01

100

A Two-locus DNA Sequence Database for Typing Plant and Human Pathogens Within the Fusarium oxysporum Species Complex  

Technology Transfer Automated Retrieval System (TEKTRAN)

We constructed a two-locus database, comprising partial translation elongation factor (EF-1alpha) gene sequences and nearly full-length sequences of the nuclear ribosomal intergenic spacer region (IGS rDNA) for 850 isolates spanning the phylogenetic breadth of the Fusarium oxysporum species complex ...

101

Documentation for the U.S. Geological Survey Public-Supply Database (PSDB): a database of permitted public-supply wells, surface-water intakes, and systems in the United States  

USGS Publications Warehouse

The purpose of this report is to document the PSDB and explain the methods used to populate and update the data from the SDWIS, State datasets, and map and geospatial imagery. This report describes 3 data tables and 11 domain tables, including field contents, data sources, and relations between tables. Although the PSDB database is not available to the general public, this information should be useful for others who are developing other database systems to store and analyze public-supply system and facility data.

Price, Curtis V.; Maupin, Molly A.

2014-01-01

102

MethBank: a database integrating next-generation sequencing single-base-resolution DNA methylation programming data.  

PubMed

DNA methylation plays crucial roles during embryonic development. Here we present MethBank (http://dnamethylome.org), a DNA methylome programming database that integrates the genome-wide single-base nucleotide methylomes of gametes and early embryos in different model organisms. Unlike extant relevant databases, MethBank incorporates the whole-genome single-base-resolution methylomes of gametes and early embryos at multiple different developmental stages in zebrafish and mouse. MethBank allows users to retrieve methylation levels, differentially methylated regions, CpG islands, gene expression profiles and genetic polymorphisms for a specific gene or genomic region. Moreover, it offers a methylome browser that is capable of visualizing high-resolution DNA methylation profiles as well as other related data in an interactive manner and thus is of great helpfulness for users to investigate methylation patterns and changes of gametes and early embryos at different developmental stages. Ongoing efforts are focused on incorporation of methylomes and related data from other organisms. Together, MethBank features integration and visualization of high-resolution DNA methylation data as well as other related data, enabling identification of potential DNA methylation signatures in different developmental stages and accordingly providing an important resource for the epigenetic and developmental studies. PMID:25294826

Zou, Dong; Sun, Shixiang; Li, Rujiao; Liu, Jiang; Zhang, Jing; Zhang, Zhang

2015-01-28

103

DISTRIBUTED STRUCTURE-SEARCHABLE TOXICITY (DSSTOX) DATABASE NETWORK: MAKING PUBLIC TOXICITY DATA RESOURCES MORE ACCESSIBLE AND USABLE FOR DATA EXPLORATION AND SAR DEVELOPMENT  

EPA Science Inventory

Distributed Structure-Searchable Toxicity (DSSTox) Database Network: Making Public Toxicity Data Resources More Accessible and U sable for Data Exploration and SAR Development Many sources of public toxicity data are not currently linked to chemical structure, are not ...

104

SkyDOT: a publicly accessible variability database, containing multiple sky surveys and real-time data  

SciTech Connect

SkyDOT (Sky Database for Objects in Time-Domain) is a Virtual Observatory currently comprised of data from the RAPTOR, ROTSE I, and OGLE I1 survey projects. This makes it a very large time domain database. In addition, the RAPTOR project provides SkyDOT with real-time variability data as well as stereoscopic information. With its web interface, we believe SkyDOT will be a very useful tool for both astronomers, and the public. Our main task has been to construct an efficient relational database containing all existing data, while handling a real-time inflow of data. We also provide a useful web interface allowing easy access to both astronomers and the public. Initially, this server will allow common searches, specific queries, and access to light curves. In the future we will include machine learning classification tools and access to spectral information.

Starr, D. L. (Dan L.); Wozniak, P. R. (Przemyslaw R.); Vestrand, W. T. (W. Thomas)

2002-01-01

105

Searching for first-degree familial relationships in California's offender DNA database: Validation of a likelihood ratio-based approach  

Microsoft Academic Search

A validation study was performed to measure the effectiveness of using a likelihood ratio-based approach to search for possible first-degree familial relationships (full-sibling and parent–child) by comparing an evidence autosomal short tandem repeat (STR) profile to California's ?1,000,000-profile State DNA Index System (SDIS) database. Test searches used autosomal STR and Y-STR profiles generated for 100 artificial test families. When the

Steven P. Myers; Mark D. Timken; Matthew L. Piucci; Gary A. Sims; Michael A. Greenwald; James J. Weigand; Kenneth C. Konzak; Martin R. Buoncristiani

2011-01-01

106

UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein–DNA interactions  

E-print Network

The Universal PBM Resource for Oligonucleotide-Binding Evaluation (UniPROBE) database is a centralized repository of information on the DNA-binding preferences of proteins as determined by universal protein-binding microarray ...

Bulyk, Martha L.

107

Potential translational targets revealed by linking mouse grooming behavioral phenotypes to gene expression using public databases  

PubMed Central

Rodent self-grooming is an important, evolutionarily conserved behavior, highly sensitive to pharmacological and genetic manipulations. Mice with aberrant grooming phenotypes are currently used to model various human disorders. Therefore, it is critical to understand the biology of grooming behavior, and to assess its translational validity to humans. The present in-silico study used publicly available gene expression and behavioral data obtained from several inbred mouse strains in the open-field, light-dark box, elevated plus- and elevated zero-maze tests. As grooming duration differed between strains, our analysis revealed several candidate genes with significant correlations between gene expression in the brain and grooming duration. The Allen Brain Atlas, STRING, GoMiner and Mouse Genome Informatics databases were used to functionally map and analyze these candidate mouse genes against their human orthologs, assessing the strain ranking of their expression and the regional distribution of expression in the mouse brain. This allowed us to identify an interconnected network of candidate genes (which have expression levels that correlate with grooming behavior), display altered patterns of expression in key brain areas related to grooming, and underlie important functions in the brain. Collectively, our results demonstrate the utility of large-scale, high-throughput data-mining and in-silico modeling for linking genomic and behavioral data, as well as their potential to identify novel neural targets for complex neurobehavioral phenotypes, including grooming. PMID:23123364

Roth, Andrew; Kyzar, Evan; Cachat, Jonathan; Stewart, Adam Michael; Green, Jeremy; Gaikwad, Siddharth; O’Leary, Timothy P.; Tabakoff, Boris; Brown, Richard E.; Kalueff, Allan V.

2014-01-01

108

Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics.  

PubMed

We report 80,388 ESTs from 23 Atlantic salmon (Salmo salar) cDNA libraries (61,819 ESTs), 6 rainbow trout (Oncorhynchus mykiss) cDNA libraries (14,544 ESTs), 2 chinook salmon (Oncorhynchus tshawytscha) cDNA libraries (1317 ESTs), 2 sockeye salmon (Oncorhynchus nerka) cDNA libraries (1243 ESTs), and 2 lake whitefish (Coregonus clupeaformis) cDNA libraries (1465 ESTs). The majority of these are 3' sequences, allowing discrimination between paralogs arising from a recent genome duplication in the salmonid lineage. Sequence assembly reveals 28,710 different S. salar, 8981 O. mykiss, 1085 O. tshawytscha, 520 O. nerka, and 1176 C. clupeaformis putative transcripts. We annotate the submitted portion of our EST database by molecular function. Higher- and lower-molecular-weight fractions of libraries are shown to contain distinct gene sets, and higher rates of gene discovery are associated with higher-molecular weight libraries. Pyloric caecum library group annotations indicate this organ may function in redox control and as a barrier against systemic uptake of xenobiotics. A microarray is described, containing 7356 salmonid elements representing 3557 different cDNAs. Analyses of cross-species hybridizations to this cDNA microarray indicate that this resource may be used for studies involving all salmonids. PMID:14962987

Rise, Matthew L; von Schalburg, Kristian R; Brown, Gordon D; Mawer, Melanie A; Devlin, Robert H; Kuipers, Nathanael; Busby, Maura; Beetz-Sargent, Marianne; Alberto, Roberto; Gibbs, A Ross; Hunt, Peter; Shukin, Robert; Zeznik, Jeffrey A; Nelson, Colleen; Jones, Simon R M; Smailus, Duane E; Jones, Steven J M; Schein, Jacqueline E; Marra, Marco A; Butterfield, Yaron S N; Stott, Jeff M; Ng, Siemon H S; Davidson, William S; Koop, Ben F

2004-03-01

109

Construction of a Public CHO Cell Line Transcript Database Using Versatile Bioinformatics Analysis Pipelines  

PubMed Central

Chinese hamster ovary (CHO) cell lines represent the most commonly used mammalian expression system for the production of therapeutic proteins. In this context, detailed knowledge of the CHO cell transcriptome might help to improve biotechnological processes conducted by specific cell lines. Nevertheless, very few assembled cDNA sequences of CHO cells were publicly released until recently, which puts a severe limitation on biotechnological research. Two extended annotation systems and web-based tools, one for browsing eukaryotic genomes (GenDBE) and one for viewing eukaryotic transcriptomes (SAMS), were established as the first step towards a publicly usable CHO cell genome/transcriptome analysis platform. This is complemented by the development of a new strategy to assemble the ca. 100 million reads, sequenced from a broad range of diverse transcripts, to a high quality CHO cell transcript set. The cDNA libraries were constructed from different CHO cell lines grown under various culture conditions and sequenced using Roche/454 and Illumina sequencing technologies in addition to sequencing reads from a previous study. Two pipelines to extend and improve the CHO cell line transcripts were established. First, de novo assemblies were carried out with the Trinity and Oases assemblers, using varying k-mer sizes. The resulting contigs were screened for potential CDS using ESTScan. Redundant contigs were filtered out using cd-hit-est. The remaining CDS contigs were re-assembled with CAP3. Second, a reference-based assembly with the TopHat/Cufflinks pipeline was performed, using the recently published draft genome sequence of CHO-K1 as reference. Additionally, the de novo contigs were mapped to the reference genome using GMAP and merged with the Cufflinks assembly using the cuffmerge software. With this approach 28,874 transcripts located on 16,492 gene loci could be assembled. Combining the results of both approaches, 65,561 transcripts were identified for CHO cell lines, which could be clustered by sequence identity into 17,598 gene clusters. PMID:24427317

Rupp, Oliver; Becker, Jennifer; Brinkrolf, Karina; Timmermann, Christina; Borth, Nicole; Pühler, Alfred; Noll, Thomas; Goesmann, Alexander

2014-01-01

110

MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools  

Microsoft Academic Search

Background: Processing raw DNA sequence data is an especially challenging task for relatively small laboratories and core facilities that produce as many as 5000 or more DNA sequences per week from multiple projects in widely differing species. To meet this challenge, we have developed the flexible, scalable, and automated sequence processing package described here. Results: MAGIC-SPP is a DNA sequence

Chun Liang; Feng Sun; Haiming Wang; Junfeng Qu; Robert M. Freeman Jr; Lee H. Pratt; Marie-michèle Cordonnier-pratt

2006-01-01

111

Expanding the functional human mitochondrial DNA database by the establishment of primate xenomitochondrial?cybrids  

PubMed Central

The nuclear and mitochondrial genomes coevolve to optimize approximately 100 different interactions necessary for an efficient ATP-generating system. This coevolution led to a species-specific compatibility between these genomes. We introduced mitochondrial DNA (mtDNA) from different primates into mtDNA-less human cells and selected for growth of cells with a functional oxidative phosphorylation system. mtDNA from common chimpanzee, pigmy chimpanzee, and gorilla were able to restore oxidative phosphorylation in the context of a human nuclear background, whereas mtDNA from orangutan, and species representative of Old-World monkeys, New-World monkeys, and lemurs were not. Oxygen consumption, a sensitive index of respiratory function, showed that mtDNA from chimpanzee, pigmy chimpanzee, and gorilla replaced the human mtDNA and restored respiration to essentially normal levels. Mitochondrial protein synthesis was also unaltered in successful “xenomitochondrial cybrids.” The abrupt failure of mtDNA from primate species that diverged from humans as recently as 8–18 million years ago to functionally replace human mtDNA suggests the presence of one or a few mutations affecting critical nuclear–mitochondrial genome interactions between these species. These cellular systems provide a demonstration of intergenus mtDNA transfer, expand more than 20-fold the number of mtDNA polymorphisms that can be analyzed in a human nuclear background, and provide a novel model for the study of nuclear–mitochondrial interactions. PMID:9256447

Kenyon, Lesley; Moraes, Carlos T.

1997-01-01

112

A two-locus DNA sequence database for identifying host-specific pathogens and phylogenetic diversity within the Fusarium oxysporum species complex  

Technology Transfer Automated Retrieval System (TEKTRAN)

An electronically portable two-locus DNA sequence database, comprising partial sequences of the translation elongation factor gene (EF-1a, 634 bp alignment) and nearly complete sequences of the nuclear ribosomal intergenic spacer region (IGS rDNA, 2220 bp alignment) for 850 isolates spanning the phy...

113

The ICRP database of dose coefficients: Workers and members of the public, version 1.0, an extension of ICRP publications 68 and 72  

SciTech Connect

A CDROM database that gives dose coefficients for inhalation and ingestion of over 800 radionuclides of 91 elements. Inhalation dose coefficients are provided for ten aerosol sizes from 0.001 {micro}m to 10 {micro}m AMAD. Effective dose and equivalent dose coefficients are given for ten integration periods form 1 d to 70 y. Extensive help files summarizing the biokinetic models in ICRP Reports 68 and 72 are provided. The greatest value added in this CDROM, however, is the powerful help utility. These files contain test from ICRP Publications 68 and 72, diagrams of the biokinetic models, and information concerning the database. The text of Publication 68 provides a very useful summary of the ICRP respiratory tract model. Hypertext links are provided for important definitions and tables, making the CDROM much more user-friendly than the original publication. Another help file compiles all of the most recent biokinetic models for systemic activity. This is particularly useful since some have been revised recently (e.g., cesium appears in Publication 56) while others have remained unchanged since Publication 30. Consolidating these models in a single place should relieve the problem of crosschecking to assure that the most current model is being used in a dose assessment.

Vargo, G.J.

2000-03-01

114

PepBank - a database of peptides based on sequence text mining and public peptide data sources  

Microsoft Academic Search

Background: Peptides are important molecules with diverse biological functions and biomedical uses. To date, there does not exist a single, searchable archive for peptide sequences or associated biological data. Rather, peptide sequences still have to be mined from abstracts and full-length articles, and\\/or obtained from the fragmented public sources. Description: We have constructed a new database (PepBank), which at the

Timur Shtatland; Daniel Guettler; Misha Kossodo; Misha Pivovarov; Ralph Weissleder

2007-01-01

115

The TTSMI database: a catalog of triplex target DNA sites associated with genes and regulatory elements in the human genome.  

PubMed

A triplex target DNA site (TTS), a stretch of DNA that is composed of polypurines, is able to form a triple-helix (triplex) structure with triplex-forming oligonucleotides (TFOs) and is able to influence the site-specific modulation of gene expression and/or the modification of genomic DNA. The co-localization of a genomic TTS with gene regulatory signals and functional genome structures suggests that TFOs could potentially be exploited in antigene strategies for the therapy of cancers and other genetic diseases. Here, we present the TTS Mapping and Integration (TTSMI; http://ttsmi.bii.a-star.edu.sg) database, which provides a catalog of unique TTS locations in the human genome and tools for analyzing the co-localization of TTSs with genomic regulatory sequences and signals that were identified using next-generation sequencing techniques and/or predicted by computational models. TTSMI was designed as a user-friendly tool that facilitates (i) fast searching/filtering of TTSs using several search terms and criteria associated with sequence stability and specificity, (ii) interactive filtering of TTSs that co-localize with gene regulatory signals and non-B DNA structures, (iii) exploration of dynamic combinations of the biological signals of specific TTSs and (iv) visualization of a TTS simultaneously with diverse annotation tracks via the UCSC genome browser. PMID:25324314

Jenjaroenpun, Piroon; Chew, Chee Siang; Yong, Tai Pang; Choowongkomon, Kiattawee; Thammasorn, Wimada; Kuznetsov, Vladimir A

2015-01-28

116

Use of DNA profiles for investigation using a simulated national DNA database: Part II. Statistical and ethical considerations on familial searching.  

PubMed

Familial searching consists of searching for a full profile left at a crime scene in a National DNA Database (NDNAD). In this paper we are interested in the circumstance where no full match is returned, but a partial match is found between a database member's profile and the crime stain. Because close relatives share more of their DNA than unrelated persons, this partial match may indicate that the crime stain was left by a close relative of the person with whom the partial match was found. This approach has successfully solved important crimes in the UK and the USA. In a previous paper, a model, which takes into account substructure and siblings, was used to simulate a NDNAD. In this paper, we have used this model to test the usefulness of familial searching and offer guidelines for pre-assessment of the cases based on the likelihood ratio. Siblings of "persons" present in the simulated Swiss NDNAD were created. These profiles (N=10,000) were used as traces and were then compared to the whole database (N=100,000). The statistical results obtained show that the technique has great potential confirming the findings of previous studies. However, effectiveness of the technique is only one part of the story. Familial searching has juridical and ethical aspects that should not be ignored. In Switzerland for example, there are no specific guidelines to the legality or otherwise of familial searching. This article both presents statistical results, and addresses criminological and civil liberties aspects to take into account risks and benefits of familial searching. PMID:20457057

Hicks, T; Taroni, F; Curran, J; Buckleton, J; Castella, V; Ribaux, O

2010-10-01

117

Searching for first-degree familial relationships in California's offender DNA database: validation of a likelihood ratio-based approach.  

PubMed

A validation study was performed to measure the effectiveness of using a likelihood ratio-based approach to search for possible first-degree familial relationships (full-sibling and parent-child) by comparing an evidence autosomal short tandem repeat (STR) profile to California's ?1,000,000-profile State DNA Index System (SDIS) database. Test searches used autosomal STR and Y-STR profiles generated for 100 artificial test families. When the test sample and the first-degree relative in the database were characterized at the 15 Identifiler(®) (Applied Biosystems(®), Foster City, CA) STR loci, the search procedure included 96% of the fathers and 72% of the full-siblings. When the relative profile was limited to the 13 Combined DNA Index System (CODIS) core loci, the search procedure included 93% of the fathers and 61% of the full-siblings. These results, combined with those of functional tests using three real families, support the effectiveness of this tool. Based upon these results, the validated approach was implemented as a key, pragmatic and demonstrably practical component of the California Department of Justice's Familial Search Program. An investigative lead created through this process recently led to an arrest in the Los Angeles Grim Sleeper serial murders. PMID:21056023

Myers, Steven P; Timken, Mark D; Piucci, Matthew L; Sims, Gary A; Greenwald, Michael A; Weigand, James J; Konzak, Kenneth C; Buoncristiani, Martin R

2011-11-01

118

The MOSART database: linking the SART CORS clinical database to the population-based Massachusetts PELL reproductive public health data system.  

PubMed

Although Assisted Reproductive Technology (ART) births make up 1.6 % of births in the US, the impact of ART on subsequent infant and maternal health is not well understood. Clinical ART treatment records linked to population data would be a powerful tool to study long term outcomes among those treated or not by ART. This paper describes the development of a database intended to accomplish this task. We constructed the Massachusetts Outcomes Study of Assisted Reproductive Technology (MOSART) database by linking the Society of Assisted Reproductive Technologies Clinical Outcomes Reporting System (SART CORS) and the Massachusetts (MA) Pregnancy to Early Life Longitudinal (PELL) data systems for children born to MA resident women at MA hospitals between July 2004 and December 2008. PELL data representing 282,971 individual women and their 334,152 deliveries and 342,035 total births were linked with 48,578 cycles of ART treatment in SART CORS delivered to MA residents or women receiving treatment in MA clinics, representing 18,439 eligible women of whom 9,326 had 10,138 deliveries in this time period. A deterministic five phase linkage algorithm methodology was employed. Linkage results, accuracy, and concordance analyses were examined. We linked 9,092 (89.7 %) SART CORS outcome records to PELL delivery records overall, including 95.0 % among known MA residents treated in MA clinics; 70.8 % with full exact matches. There were minimal differences between matched and unmatched delivery records, except for unknown residency and out-of-state ART site. There was very low concordance of reported use of ART treatment between SART CORS and PELL (birth certificate) data. A total of 3.4 % of MA children (11,729) were identified from ART assisted pregnancies (6,556 singletons; 5,173 multiples). The MOSART linked database provides a strong basis for further longitudinal ART outcomes studies and supports the continued development of potentially powerful linked clinical-public health databases. PMID:24623195

Kotelchuck, Milton; Hoang, Lan; Stern, Judy E; Diop, Hafsatou; Belanoff, Candice; Declercq, Eugene

2014-11-01

119

Collecting, archiving and processing DNA from wildlife samples using FTA® databasing paper  

Microsoft Academic Search

BACKGROUND: Methods involving the analysis of nucleic acids have become widespread in the fields of traditional biology and ecology, however the storage and transport of samples collected in the field to the laboratory in such a manner to allow purification of intact nucleic acids can prove problematical. RESULTS: FTA® databasing paper is widely used in human forensic analysis for the

LM Smith; LA Burgoyne

2004-01-01

120

A brief history of the formation of DNA databases in forensic science within Europe  

Microsoft Academic Search

The introduction of DNA analysis to forensic science brought with it a number of choices for analysis, not all of which were compatible. As laboratories throughout Europe were eager to use the new technology different systems became routine in different laboratories and consequently, there was no basis for the exchange of results. A period of co-operation then started in which

Peter D. Martin; Hermann Schmitter; Peter M. Schneider

2001-01-01

121

Discovery of Possible Gene Relationships through the Application of Self-Organizing Maps to DNA Microarray Databases  

PubMed Central

DNA microarrays and cell cycle synchronization experiments have made possible the study of the mechanisms of cell cycle regulation of Saccharomyces cerevisiae by simultaneously monitoring the expression levels of thousands of genes at specific time points. On the other hand, pattern recognition techniques can contribute to the analysis of such massive measurements, providing a model of gene expression level evolution through the cell cycle process. In this paper, we propose the use of one of such techniques –an unsupervised artificial neural network called a Self-Organizing Map (SOM)–which has been successfully applied to processes involving very noisy signals, classifying and organizing them, and assisting in the discovery of behavior patterns without requiring prior knowledge about the process under analysis. As a test bed for the use of SOMs in finding possible relationships among genes and their possible contribution in some biological processes, we selected 282 S. cerevisiae genes that have been shown through biological experiments to have an activity during the cell cycle. The expression level of these genes was analyzed in five of the most cited time series DNA microarray databases used in the study of the cell cycle of this organism. With the use of SOM, it was possible to find clusters of genes with similar behavior in the five databases along two cell cycles. This result suggested that some of these genes might be biologically related or might have a regulatory relationship, as was corroborated by comparing some of the clusters obtained with SOMs against a previously reported regulatory network that was generated using biological knowledge, such as protein-protein interactions, gene expression levels, metabolism dynamics, promoter binding, and modification, regulation and transport of proteins. The methodology described in this paper could be applied to the study of gene relationships of other biological processes in different organisms. PMID:24699245

Chavez-Alvarez, Rocio; Chavoya, Arturo; Mendez-Vazquez, Andres

2014-01-01

122

Discovery of possible gene relationships through the application of self-organizing maps to DNA microarray databases.  

PubMed

DNA microarrays and cell cycle synchronization experiments have made possible the study of the mechanisms of cell cycle regulation of Saccharomyces cerevisiae by simultaneously monitoring the expression levels of thousands of genes at specific time points. On the other hand, pattern recognition techniques can contribute to the analysis of such massive measurements, providing a model of gene expression level evolution through the cell cycle process. In this paper, we propose the use of one of such techniques--an unsupervised artificial neural network called a Self-Organizing Map (SOM)-which has been successfully applied to processes involving very noisy signals, classifying and organizing them, and assisting in the discovery of behavior patterns without requiring prior knowledge about the process under analysis. As a test bed for the use of SOMs in finding possible relationships among genes and their possible contribution in some biological processes, we selected 282 S. cerevisiae genes that have been shown through biological experiments to have an activity during the cell cycle. The expression level of these genes was analyzed in five of the most cited time series DNA microarray databases used in the study of the cell cycle of this organism. With the use of SOM, it was possible to find clusters of genes with similar behavior in the five databases along two cell cycles. This result suggested that some of these genes might be biologically related or might have a regulatory relationship, as was corroborated by comparing some of the clusters obtained with SOMs against a previously reported regulatory network that was generated using biological knowledge, such as protein-protein interactions, gene expression levels, metabolism dynamics, promoter binding, and modification, regulation and transport of proteins. The methodology described in this paper could be applied to the study of gene relationships of other biological processes in different organisms. PMID:24699245

Chavez-Alvarez, Rocio; Chavoya, Arturo; Mendez-Vazquez, Andres

2014-01-01

123

Automatic detection of lung nodules in computed tomography images: training and validation of algorithms using public research databases  

NASA Astrophysics Data System (ADS)

Lung cancer is one of the main public health issues in developed countries. Lung cancer typically manifests itself as non-calcified pulmonary nodules that can be detected reading lung Computed Tomography (CT) images. To assist radiologists in reading images, researchers started, a decade ago, the development of Computer Aided Detection (CAD) methods capable of detecting lung nodules. In this work, a CAD composed of two CAD subprocedures is presented: , devoted to the identification of parenchymal nodules, and , devoted to the identification of the nodules attached to the pleura surface. Both CADs are an upgrade of two methods previously presented as Voxel Based Neural Approach CAD . The novelty of this paper consists in the massive training using the public research Lung International Database Consortium (LIDC) database and on the implementation of new features for classification with respect to the original VBNA method. Finally, the proposed CAD is blindly validated on the ANODE09 dataset. The result of the validation is a score of 0.393, which corresponds to the average sensitivity of the CAD computed at seven predefined false positive rates: 1/8, 1/4, 1/2, 1, 2, 4, and 8 FP/CT.

Camarlinghi, Niccolò

2013-09-01

124

DNA DNA DNA (d)DNA DNA DNA  

E-print Network

DNA DNA DNA DNA DNA DNA DNA DNA [ 2008] (d)DNA DNA DNA DNA 2 3 DNA DNA DNA DNA DNA DNA DNA (a) (c) (b) (d) #12;DNA DNA DNA DNA DNA DNA DNA DNA (b) DNA [Tanaka et al.2008] DNA DNA DNA DNA DNA DNA DNA #12;iGEM MIT MIT

Hagiya, Masami

125

A database of 32 DNA triplets to study triple helices by molecular mechanics and dynamics.  

PubMed

We present here a database of 32 deoxyribonucleotide triplets, that can be used as building blocks of triple helix forming deoxyribonucleotides on a computer. This database is made of all the pairing schemes of the triplets ATT, GCC+, ATA and GCG where the third base forms two hydrogen bonds with the purine of the first two Watson-Crick strands. The essential features of the known triple helices were preserved in the resulting structures. A triple helix can be easily built from any combination of these basic triplets. Four homogeneous and alternate triple helices thus obtained were studied by molecular mechanics and dynamics in vacuo. The results are in agreement with known experimental observations for ATT and suggest a possible structure for the GCG triple helix. In order to characterize the geometry of the structures obtained, the definitions of nucleic acid structure parameters (R.E. Dickerson et al., EMBO J. 8 (1989) 1-4) have been extended to triple helical polynucleotides. PMID:8011951

Piriou, J M; Ketterlé, C; Gabarro-Arpa, J; Cognet, J A; Le Bret, M

1994-06-01

126

An analysis of the success rate of 908 trace DNA samples submitted to the Crime Sample Database Unit in New Zealand  

Microsoft Academic Search

The Crime Sample Database Unit, part of the Forensic Biology group at the Institute of Environmental Science and Research Limited, receives samples predominantly from unsolved volume crime cases, such as burglaries and car theft, for inclusion on the New Zealand National DNA Databank. A high proportion of these samples are analysed for the presence of low or trace amounts of

SallyAnn Harbison; Marita Fallow; Donna Bushell

2008-01-01

127

Assessing the impact of paediatric oncology publications using three citation databases.  

PubMed

Despite some reported limitations, Web of Science has been the standard source to assess the impact of individual articles, and consequently journals. By analysing the citations to articles published in the field of paediatric oncology, we demonstrate that Scopus and Google Scholar, the two new citation databases, retrieve more citations than Web of Science. The strength of Scopus lies in identifying non-English literature from Western and Eastern Europe, while Google Scholar is proficient at identifying English and non-English literature from Africa, Asia and Central and South America. These findings have implications for researchers, journals and health libraries. PMID:20922764

Arora, Ramandeep S; Eden, Tim O B

2011-01-01

128

BrassicaTED - a public database for utilization of miniature transposable elements in Brassica species  

PubMed Central

Background MITE, TRIM and SINEs are miniature form transposable elements (mTEs) that are ubiquitous and dispersed throughout entire plant genomes. Tens of thousands of members cause insertion polymorphism at both the inter- and intra- species level. Therefore, mTEs are valuable targets and resources for development of markers that can be utilized for breeding, genetic diversity and genome evolution studies. Taking advantage of the completely sequenced genomes of Brassica rapa and B. oleracea, characterization of mTEs and building a curated database are prerequisite to extending their utilization for genomics and applied fields in Brassica crops. Findings We have developed BrassicaTED as a unique web portal containing detailed characterization information for mTEs of Brassica species. At present, BrassicaTED has datasets for 41 mTE families, including 5894 and 6026 members from 20 MITE families, 1393 and 1639 members from 5 TRIM families, 1270 and 2364 members from 16 SINE families in B. rapa and B. oleracea, respectively. BrassicaTED offers different sections to browse structural and positional characteristics for every mTE family. In addition, we have added data on 289 MITE insertion polymorphisms from a survey of seven Brassica relatives. Genes with internal mTE insertions are shown with detailed gene annotation and microarray-based comparative gene expression data in comparison with their paralogs in the triplicated B. rapa genome. This database also includes a novel tool, K BLAST (Karyotype BLAST), for clear visualization of the locations for each member in the B. rapa and B. oleracea pseudo-genome sequences. Conclusions BrassicaTED is a newly developed database of information regarding the characteristics and potential utility of mTEs including MITE, TRIM and SINEs in B. rapa and B. oleracea. The database will promote the development of desirable mTE-based markers, which can be utilized for genomics and breeding in Brassica species. BrassicaTED will be a valuable repository for scientists and breeders, promoting efficient research on Brassica species. BrassicaTED can be accessed at http://im-crop.snu.ac.kr/BrassicaTED/index.php. PMID:24948109

2014-01-01

129

Seabird databases and the new paradigm for scientific publication and attribution  

USGS Publications Warehouse

For more than 300 years, the peer-reviewed journal article has been the principal medium for packaging and delivering scientific data. With new tools for managing digital data, a new paradigm is emerging—one that demands open and direct access to data and that enables and rewards a broad-based approach to scientific questions. Ground-breaking papers in the future will increasingly be those that creatively mine and synthesize vast stores of data available on the Internet. This is especially true for conservation science, in which essential data can be readily captured in standard record formats. For seabird professionals, a number of globally shared databases are in the offing, or should be. These databases will capture the salient results of inventories and monitoring, pelagic surveys, diet studies, and telemetry. A number of real or perceived barriers to data sharing exist, but none is insurmountable. Our discipline should take an important stride now by adopting a specially designed markup language for annotating and sharing seabird data.

Hatch, Scott A.

2010-01-01

130

Amplification volume reduction on DNA database samples using FTA™ Classic Cards.  

PubMed

The DNA forensic community always strives towards improvements in aspects such as sensitivity, robustness, and efficacy balanced with cost efficiency. Therefore our laboratory decided to study the feasibility of PCR amplification volume reduction using DNA entrapped in FTA™ Classic Card and to bring cost savings to the laboratory. There were a few concerns the laboratory needed to address. First, the kinetics of the amplification reaction could be significantly altered. Second, an increase in sensitivity might affect interpretation due to increased stochastic effects even though they were pristine samples. Third, statics might cause FTA punches to jump out of its allocated well into another thus causing sample-to-sample contamination. Fourth, the size of the punches might be too small for visual inspection. Last, there would be a limit to the extent of volume reduction due to evaporation and the possible need of re-injection of samples for capillary electrophoresis. The laboratory had successfully optimized a reduced amplification volume of 10 ?L for FTA samples. PMID:21543276

Wong, Hang Yee; Lim, Eng Seng Simon; Tan-Siew, Wai Fun

2012-03-01

131

Insights from the DNA databases: approaches to the phylogenetic structure of Acanthamoeba.  

PubMed

Species of Acanthamoeba have been traditionally described using morphology (primarily cyst structure), or cytology of nuclear division (used by Pussard and Pons, 1977). Twenty-plus putative species were proposed based on such criteria. Morphology, however, is often plastic, dependent upon culture conditions. DNA sequences of the nuclear small subunit (18S) rRNA that can be used for the study of the phylogeny of Acanthamoeba have increased from a single sequence in 1986 to more than 1800 in 2013. Some of the patterns of the sequence data for Acanthamoeba are reviewed, and some of the insights that this data illuminates are illustrated. In particular, the data suggest the existence of 20 or more genotypic types, a number not dissimilar to the number of named species of Acanthamoeba. However, molecular studies make clear that the relationship between phylogenetic relatedness and species names as we know them for Acanthamoeba is tenuous at best. PMID:24999094

Fuerst, Paul A

2014-11-01

132

Does language matter? A case study of epidemiological and public health journals, databases and professional education in French, German and Italian  

PubMed Central

Epidemiology and public health are usually context-specific. Journals published in different languages and countries play a role both as sources of data and as channels through which evidence is incorporated into local public health practice. Databases in these languages facilitate access to relevant journals, and professional education in these languages facilitates the growth of native expertise in epidemiology and public health. However, as English has become the lingua franca of scientific communication in the era of globalisation, many journals published in non-English languages face the difficult dilemma of either switching to English and competing internationally, or sticking to the native tongue and having a restricted circulation among a local readership. This paper discusses the historical development of epidemiology and the current scene of epidemiological and public health journals, databases and professional education in three Western European languages: French, German and Italian, and examines the dynamics and struggles they have today. PMID:18826570

Baussano, Iacopo; Brzoska, Patrick; Fedeli, Ugo; Larouche, Claudia; Razum, Oliver; Fung, Isaac C-H

2008-01-01

133

Creating a data exchange strategy for radiotherapy research: towards federated databases and anonymised public datasets.  

PubMed

Disconnected cancer research data management and lack of information exchange about planned and ongoing research are complicating the utilisation of internationally collected medical information for improving cancer patient care. Rapidly collecting/pooling data can accelerate translational research in radiation therapy and oncology. The exchange of study data is one of the fundamental principles behind data aggregation and data mining. The possibilities of reproducing the original study results, performing further analyses on existing research data to generate new hypotheses or developing computational models to support medical decisions (e.g. risk/benefit analysis of treatment options) represent just a fraction of the potential benefits of medical data-pooling. Distributed machine learning and knowledge exchange from federated databases can be considered as one beyond other attractive approaches for knowledge generation within "Big Data". Data interoperability between research institutions should be the major concern behind a wider collaboration. Information captured in electronic patient records (EPRs) and study case report forms (eCRFs), linked together with medical imaging and treatment planning data, are deemed to be fundamental elements for large multi-centre studies in the field of radiation therapy and oncology. To fully utilise the captured medical information, the study data have to be more than just an electronic version of a traditional (un-modifiable) paper CRF. Challenges that have to be addressed are data interoperability, utilisation of standards, data quality and privacy concerns, data ownership, rights to publish, data pooling architecture and storage. This paper discusses a framework for conceptual packages of ideas focused on a strategic development for international research data exchange in the field of radiation therapy and oncology. PMID:25458128

Skripcak, Tomas; Belka, Claus; Bosch, Walter; Brink, Carsten; Brunner, Thomas; Budach, Volker; Büttner, Daniel; Debus, Jürgen; Dekker, Andre; Grau, Cai; Gulliford, Sarah; Hurkmans, Coen; Just, Uwe; Krause, Mechthild; Lambin, Philippe; Langendijk, Johannes A; Lewensohn, Rolf; Lühr, Armin; Maingon, Philippe; Masucci, Michele; Niyazi, Maximilian; Poortmans, Philip; Simon, Monique; Schmidberger, Heinz; Spezi, Emiliano; Stuschke, Martin; Valentini, Vincenzo; Verheij, Marcel; Whitfield, Gillian; Zackrisson, Björn; Zips, Daniel; Baumann, Michael

2014-12-01

134

ENVIRONMENTAL RESIDUE EFFECTS DATABASE (ERED)  

EPA Science Inventory

US Army Corps of Engineers public web site for the "Environmental Residue Effects Database", a searchable database of adverse biological effects associated with tissue concentrations of various contaminants....

135

Complementary Value of Databases for Discovery of Scholarly Literature A User Survey of On-Line Searching for Publications in Art History  

Microsoft Academic Search

Discovery of academic literature through Web search engines challenges the traditional role of specialized research databases. Creation of literature outside of academic presses and peer- reviewed publications expands the content for scholarly research within a particular field. The resulting body of literature raises the question of whether scholars prefer the perceived broader access of Web search engines or opt for

Erik Nemeth

136

Exploration of preterm birth rates using the public health exposome database and computational analysis methods.  

PubMed

Recent advances in informatics technology has made it possible to integrate, manipulate, and analyze variables from a wide range of scientific disciplines allowing for the examination of complex social problems such as health disparities. This study used 589 county-level variables to identify and compare geographical variation of high and low preterm birth rates. Data were collected from a number of publically available sources, bringing together natality outcomes with attributes of the natural, built, social, and policy environments. Singleton early premature county birth rate, in counties with population size over 100,000 persons provided the dependent variable. Graph theoretical techniques were used to identify a wide range of predictor variables from various domains, including black proportion, obesity and diabetes, sexually transmitted infection rates, mother's age, income, marriage rates, pollution and temperature among others. Dense subgraphs (paracliques) representing groups of highly correlated variables were resolved into latent factors, which were then used to build a regression model explaining prematurity (R-squared = 76.7%). Two lists of counties with large positive and large negative residuals, indicating unusual prematurity rates given their circumstances, may serve as a starting point for ways to intervene and reduce health disparities for preterm births. PMID:25464130

Kershenbaum, Anne D; Langston, Michael A; Levine, Robert S; Saxton, Arnold M; Oyana, Tonny J; Kilbourne, Barbara J; Rogers, Gary L; Gittner, Lisaann S; Baktash, Suzanne H; Matthews-Juarez, Patricia; Juarez, Paul D

2014-12-01

137

Exploration of Preterm Birth Rates Using the Public Health Exposome Database and Computational Analysis Methods  

PubMed Central

Recent advances in informatics technology has made it possible to integrate, manipulate, and analyze variables from a wide range of scientific disciplines allowing for the examination of complex social problems such as health disparities. This study used 589 county-level variables to identify and compare geographical variation of high and low preterm birth rates. Data were collected from a number of publically available sources, bringing together natality outcomes with attributes of the natural, built, social, and policy environments. Singleton early premature county birth rate, in counties with population size over 100,000 persons provided the dependent variable. Graph theoretical techniques were used to identify a wide range of predictor variables from various domains, including black proportion, obesity and diabetes, sexually transmitted infection rates, mother’s age, income, marriage rates, pollution and temperature among others. Dense subgraphs (paracliques) representing groups of highly correlated variables were resolved into latent factors, which were then used to build a regression model explaining prematurity (R-squared = 76.7%). Two lists of counties with large positive and large negative residuals, indicating unusual prematurity rates given their circumstances, may serve as a starting point for ways to intervene and reduce health disparities for preterm births. PMID:25464130

Kershenbaum, Anne D.; Langston, Michael A.; Levine, Robert S.; Saxton, Arnold M.; Oyana, Tonny J.; Kilbourne, Barbara J.; Rogers, Gary L.; Gittner, Lisaann S.; Baktash, Suzanne H.; Matthews-Juarez, Patricia; Juarez, Paul D.

2014-01-01

138

UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions.  

PubMed

The Universal PBM Resource for Oligonucleotide Binding Evaluation (UniPROBE) serves as a convenient source of information on published data generated using universal protein-binding microarray (PBM) technology, which provides in vitro data about the relative DNA-binding preferences of transcription factors for all possible sequence variants of a length k ('k-mers'). The database displays important information about the proteins and displays their DNA-binding specificity data in terms of k-mers, position weight matrices and graphical sequence logos. This update to the database documents the growth of UniPROBE since the last update 4 years ago, and introduces a variety of new features and tools, including a new streamlined pipeline that facilitates data deposition by universal PBM data generators in the research community, a tool that generates putative nonbinding (i.e. negative control) DNA sequences for one or more proteins and novel motifs obtained by analyzing the PBM data using the BEEML-PBM algorithm for motif inference. The UniPROBE database is available at http://uniprobe.org. PMID:25378322

Hume, Maxwell A; Barrera, Luis A; Gisselbrecht, Stephen S; Bulyk, Martha L

2015-01-28

139

Microgravity Database  

NSDL National Science Digital Library

The European Space Agencies (ESA) Microgravity Database "gives scientists access to information regarding all experiments carried out on ESA and NASA missions by European scientists since the 1960s." Users choose from a physical or life sciences query form, then can search by experiment and investigators, mission and facility, publications and source, and more. Results provide the mission name, data, payload, research subject, publication information, an abstract, and any other available facts or related links. A very intuitive and well designed database, visitors should appreciate its unique and extensive content.

2000-01-01

140

Comparative Study of Seven Commercial Kits for Human DNA Extraction from Urine Samples Suitable for DNA Biomarker-Based Public Health Studies  

PubMed Central

Human genomic DNA extracted from urine could be an interesting tool for large-scale public health studies involving characterization of genetic variations or DNA biomarkers as a result of the simple and noninvasive collection method. These studies, involving many samples, require a rapid, easy, and standardized extraction protocol. Moreover, for practicability, there is a necessity to collect urine at a moment different from the first void and to store it appropriately until analysis. The present study compared seven commercial kits to select the most appropriate urinary human DNA extraction procedure for epidemiological studies. DNA yield has been determined using different quantification methods: two classical, i.e., NanoDrop and PicoGreen, and two species-specific real-time quantitative (q)PCR assays, as DNA extracted from urine contains, besides human, microbial DNA also, which largely contributes to the total DNA yield. In addition, the kits giving a good yield were also tested for the presence of PCR inhibitors. Further comparisons were performed regarding the sampling time and the storage conditions. Finally, as a proof-of-concept, an important gene related to smoking has been genotyped using the developed tools. We could select one well-performing kit for the human DNA extraction from urine suitable for molecular diagnostic real-time qPCR-based assays targeting genetic variations, applicable to large-scale studies. In addition, successful genotyping was possible using DNA extracted from urine stored at ?20°C for several months, and an acceptable yield could also be obtained from urine collected at different moments during the day, which is particularly important for public health studies. PMID:25365790

El Bali, Latifa; Diman, Aurélie; Bernard, Alfred; Roosens, Nancy H. C.; De Keersmaecker, Sigrid C. J.

2014-01-01

141

De-identifying a public use microdata file from the Canadian national discharge abstract database  

PubMed Central

Abstract Background The Canadian Institute for Health Information (CIHI) collects hospital discharge abstract data (DAD) from Canadian provinces and territories. There are many demands for the disclosure of this data for research and analysis to inform policy making. To expedite the disclosure of data for some of these purposes, the construction of a DAD public use microdata file (PUMF) was considered. Such purposes include: confirming some published results, providing broader feedback to CIHI to improve data quality, training students and fellows, providing an easily accessible data set for researchers to prepare for analyses on the full DAD data set, and serve as a large health data set for computer scientists and statisticians to evaluate analysis and data mining techniques. The objective of this study was to measure the probability of re-identification for records in a PUMF, and to de-identify a national DAD PUMF consisting of 10% of records. Methods Plausible attacks on a PUMF were evaluated. Based on these attacks, the 2008-2009 national DAD was de-identified. A new algorithm was developed to minimize the amount of suppression while maximizing the precision of the data. The acceptable threshold for the probability of correct re-identification of a record was set at between 0.04 and 0.05. Information loss was measured in terms of the extent of suppression and entropy. Results Two different PUMF files were produced, one with geographic information, and one with no geographic information but more clinical information. At a threshold of 0.05, the maximum proportion of records with the diagnosis code suppressed was 20%, but these suppressions represented only 8-9% of all values in the DAD. Our suppression algorithm has less information loss than a more traditional approach to suppression. Smaller regions, patients with longer stays, and age groups that are infrequently admitted to hospitals tend to be the ones with the highest rates of suppression. Conclusions The strategies we used to maximize data utility and minimize information loss can result in a PUMF that would be useful for the specific purposes noted earlier. However, to create a more detailed file with less information loss suitable for more complex health services research, the risk would need to be mitigated by requiring the data recipient to commit to a data sharing agreement. PMID:21861894

2011-01-01

142

Lung Image Databases-2  

Cancer.gov

Lung Image Database Consortium’s Normalized Relational Database • De-identified (anonymized) CT datasets • Publicly accessible • Web search tools • Cases from search results can be downloaded – ftp or DICOM De-identified CT datasets Digital Imaging and

143

AIDSinfo Drug Database  

MedlinePLUS

... Widgets Order Publications Skip Nav AIDS info Drug Database Home > Drugs Español Text Size Drugs by class ... health care providers and patients. Search the Drug Database Help × Search by drug name Performs a search ...

144

E-SovTox: An online database of the main publicly-available sources of toxicity data concerning REACH-relevant chemicals published in the Russian language.  

PubMed

A new open-access online database, E-SovTox, is presented. E-SovTox provides toxicological data for substances relevant to the EU Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH) system, from publicly-available Russian language data sources. The database contains information selected mainly from scientific journals published during the Soviet Union era. The main information source for this database - the journal, Gigiena Truda i Professional'nye Zabolevania [Industrial Hygiene and Occupational Diseases], published between 1957 and 1992 - features acute, but also chronic, toxicity data for numerous industrial chemicals, e.g. for rats, mice, guinea-pigs and rabbits. The main goal of the abovementioned toxicity studies was to derive the maximum allowable concentration limits for industrial chemicals in the occupational health settings of the former Soviet Union. Thus, articles featured in the database include mostly data on LD50 values, skin and eye irritation, skin sensitisation and cumulative properties. Currently, the E-SovTox database contains toxicity data selected from more than 500 papers covering more than 600 chemicals. The user is provided with the main toxicity information, as well as abstracts of these papers in Russian and in English (given as provided in the original publication). The search engine allows cross-searching of the database by the name or CAS number of the compound, and the author of the paper. The E-SovTox database can be used as a decision-support tool by researchers and regulators for the hazard assessment of chemical substances. PMID:20822322

Sihtmäe, Mariliis; Blinova, Irina; Aruoja, Villem; Dubourguier, Henri-Charles; Legrand, Nicolas; Kahru, Anne

2010-08-01

145

Clinical and public health research using methylated DNA immunoprecipitation (MeDIP): a comparison of commercially available kits to examine differential DNA methylation across the genome.  

PubMed

The methylated DNA immunoprecipitation method (MeDIP) is a genome-wide, high-resolution approach that detects DNA methylation with oligonucleotide tiling arrays or high throughput sequencing platforms. A simplified high-throughput MeDIP assay will enable translational research studies in clinics and populations, which will greatly enhance our understanding of the human methylome. We compared three commercial kits, MagMeDIP Kit TM (Diagenode), Methylated-DNA IP Kit (Zymo Research) and Methylamp™ Methylated DNA Capture Kit (Epigentek), in order to identify which one has better reliability and sensitivity for genomic DNA enrichment. Each kit was used to enrich two samples, one from fresh tissue and one from a cell line, with two different DNA amounts. The enrichment efficiency of each kit was evaluated by agarose gel band intensity after Nco I digestion and by reaction yield of methylated DNA. A successful enrichment is expected to have a 1:4 to 10:1 conversion ratio and a yield of 80% or higher. We also evaluated the hybridization efficiency to genome-wide methylation arrays in a separate cohort of tissue samples. We observed that the MagMeDIP kit had the highest yield for the two DNA amounts and for both the tissue and cell line samples, as well as for the positive control. In addition, the DNA was successfully enriched from a 1:4 to 10:1 ratio. Therefore, the MagMeDIP kit is a useful research tool that will enable clinical and public health genome-wide DNA methylation studies. PMID:22207357

Brebi-Mieville, Priscilla; Ili-Gangas, Carmen; Leal-Rojas, Pamela; Noordhuis, Maartje G; Soudry, Ethan; Perez, Jimena; Roa, Juan Carlos; Sidransky, David; Guerrero-Preston, Rafael

2012-01-01

146

q -gram based database searching using a suffix array (QUASAR)  

Microsoft Academic Search

With the increasing amount of DNA sequence informationdeposited in public databases, searching for similarity to aquery sequence has become a basic operation in molecularbiology. But even today's fast algorithms reach theirlimits when applied to all-versus-all comparisons of largedatabases. Here we present a new database searching algorithmcalled QUASAR (Q-gram Alignment based on SuffixARrays) which was designed to quickly detect sequenceswith strong

Stefan Burkhardt; Andreas Crauser; Paolo Ferragina; Hans-Peter Lenhof; Eric Rivals; Martin Vingron

1999-01-01

147

Drinking Water Treatability Database (Database)  

EPA Science Inventory

The drinking Water Treatability Database (TDB) will provide data taken from the literature on the control of contaminants in drinking water, and will be housed on an interactive, publicly-available USEPA web site. It can be used for identifying effective treatment processes, rec...

148

The LISS-A Public Database of Common Imaging Signs of Lung Diseases for Computer-Aided Detection and Diagnosis Research and Medical Education.  

PubMed

Lung CT imaging signs play important roles in the diagnosis of lung diseases. In this paper, we review the significance of CT imaging signs in disease diagnosis and determine the inclusion criterion of CT scans and CT imaging signs of our database. We develop the software of abnormal regions annotation and design the storage scheme of CT images and annotation data. Then we present a publicly available database of Lung CT Imaging Signs, called LISS for short, which contains 271 CT scans and 677 abnormal regions in them. The 677 abnormal regions are divided into 9 categories of common CT Imaging Signs of Lung disease (CISLs). The ground truth of these CISLs regions and the corresponding categories are provided. Furthermore, to make the database publicly available, all private data in CT scans are eliminated or replaced with provisioned values. The main characteristic of our LISS database is that it is developed from a new perspective of CT imaging signs of lung diseases instead of commonly considered lung nodules. Thus it is promising to apply to computer-aided detection and diagnosis (CAD) research and medical education. PMID:25330480

Han, Guanghui; Liu, Xiabi; Han, Feifei; Santika, I Nyoman Tenaya; Zhao, Yanfeng; Zhao, Xinming; Zhou, Chunwu

2014-10-15

149

Ku Binds Telomeric DNA in Vitro* (Received for publication, March 26, 1999, and in revised form, May 12, 1999)  

E-print Network

Ku Binds Telomeric DNA in Vitro* (Received for publication, March 26, 1999, and in revised form. Recently Ku has been shown to be a likely component of the telomeric complex in yeast, suggesting the possibility of a similar role for Ku at mammalian telomeres. However, long single- stranded G-rich overhangs

de Lange, Titia

150

The DNA Binding Properties of Saccharomyces cerevisiae Rad51 (Received for publication, June 12, 1998, and in revised form, November 16, 1998)  

E-print Network

The DNA Binding Properties of Saccharomyces cerevisiae Rad51 Protein* (Received for publication Rad51 protein is the para- digm for eukaryotic ATP-dependent DNA strand ex- change proteins. To explain some of the unique charac- teristics of DNA strand exchange promoted by Rad51 protein, when

Kowalczykowski, Stephen C.

151

A DNA Pairing-enhanced Conformation of Bacterial RecA Proteins* Received for publication, August 4, 2003, and in revised form, October 3, 2003  

E-print Network

A DNA Pairing-enhanced Conformation of Bacterial RecA Proteins* Received for publication, August 4A proteins of Escherichia coli (Ec) and Deino- coccus radiodurans (Dr) both promote a DNA strand exchange- stranded DNA-binding protein (SSB). In the absence of SSB, the initiation of strand exchange is greatly en

Cox, Michael M.

152

DNA barcoding for plants.  

PubMed

DNA barcoding uses specific regions of DNA in order to identify species. Initiatives are taking place around the world to generate DNA barcodes for all groups of living organisms and to make these data publically available in order to help understand, conserve, and utilize the world's biodiversity. For land plants the core DNA barcode markers are two sections of coding regions within the chloroplast, part of the genes, rbcL and matK. In order to create high quality databases, each plant that is DNA barcoded needs to have a herbarium voucher that accompanies the rbcL and matK DNA sequences. The quality of the DNA sequences, the primers used, and trace files should also be accessible to users of the data. Multiple individuals should be DNA barcoded for each species in order to check for errors and allow for intraspecific variation. The world's herbaria provide a rich resource of already preserved and identified material and these can be used for DNA barcoding as well as by collecting fresh samples from the wild. These protocols describe the whole DNA barcoding process, from the collection of plant material from the wild or from the herbarium, how to extract and amplify the DNA, and how to check the quality of the data after sequencing. PMID:25373752

de Vere, Natasha; Rich, Tim C G; Trinder, Sarah A; Long, Charlotte

2015-01-01

153

A New Model for Providing Cell-Free DNA and Risk Assessment for Chromosome Abnormalities in a Public Hospital Setting  

PubMed Central

Objective. Cell-free DNA (cfDNA) offers highly accurate noninvasive screening for Down syndrome. Incorporating it into routine care is complicated. We present our experience implementing a novel program for cfDNA screening, emphasizing patient education, genetic counseling, and resource management. Study Design. Beginning in January 2013, we initiated a new patient care model in which high-risk patients for aneuploidy received genetic counseling at 12 weeks of gestation. Patients were presented with four pathways for aneuploidy risk assessment and diagnosis: (1) cfDNA; (2) integrated screening; (3) direct-to-invasive testing (chorionic villus sampling or amniocentesis); or (4) no first trimester diagnostic testing/screening. Patients underwent follow-up genetic counseling and detailed ultrasound at 18–20 weeks to review first trimester testing and finalize decision for amniocentesis. Results. Counseling and second trimester detailed ultrasound were provided to 163 women. Most selected cfDNA screening (69%) over integrated screening (0.6%), direct-to-invasive testing (14.1%), or no screening (16.6%). Amniocentesis rates decreased following implementation of cfDNA screening (19.0% versus 13.0%, P < 0.05). Conclusion. When counseled about screening options, women often chose cfDNA over integrated screening. This program is a model for patient-directed, efficient delivery of a newly available high-level technology in a public health setting. Genetic counseling is an integral part of patient education and determination of plan of care. PMID:25101177

Wallerstein, Robert; Jelks, Andrea; Garabedian, Matthew J.

2014-01-01

154

Multiparameter Intelligent Monitoring in Intensive Care Ii (Mimic-Ii): A Public-Access Intensive Care Unit Database  

E-print Network

Objective: We sought to develop an intensive care unit research database applying automated techniques to aggregate high-resolution diagnostic and therapeutic data from a large, diverse population of adult intensive care ...

Saeed, Mohammed

155

Conservation of taxonomic and biological trait diversity of European stream macroinvertebrate communities: a case for a collective public database  

Microsoft Academic Search

The use of databases for the conservation of biodiversity is increasing. During the last decade, such a database has been\\u000a created for European stream macroinvertebrates. Today, it includes 527 sites that are the least human-impacted representatives\\u000a of many stream types across many European regions. It includes data on the abundance of 312 invertebrate genera, several environmental\\u000a site characteristics, collection methods,

Bernhard Statzner; Núria Bonada; Sylvain Dolédec

2007-01-01

156

Conservation of taxonomic and biological trait diversity of European stream macroinvertebrate communities: a case for a collective public database  

Microsoft Academic Search

The use of databases for the conservation of biodiversity is increasing. During the last decade, such a database has been\\u000a created for European stream macroinvertebrates. Today, it includes 527 sites that are the least human-impacted representatives\\u000a of many stream types across many European regions. It includes data on the abundance of 312 invertebrate genera, several environmental\\u000a site characteristics, collection methods,

Bernhard Statzner; Núria Bonada; Sylvain Dolédec

157

THE PUBLIC DOMAIN DATABASE ON NUCLEAR FUEL PERFORMANCE EXPERIMENTS (IFPE) FOR THE PURPOSE OF CODE DEVELOPMENT AND VALIDATION  

Microsoft Academic Search

The paper describes the compilation and maintenance of a database on nuclear fuel performance for the purpose of code development and validation. This work is carried out in close cooperation and coordination between the OECD\\/NEA, the IAEA and the IFE\\/OECD\\/Halden Reactor Project. The paper outlines the background behind the formation of the database and the progress made to date in

P. Menut; E. Sartori; J. A. Turnbull

158

GEOBASE: Israel Regional Database  

NSDL National Science Digital Library

GEOBASE is a searchable database that contains data extracted from Israel's Central Bureau of Statistics, statistical publications, public service records, local databases, and summaries from individual level datasets. GEOBASE provides regularly updated annual and quarterly series on numerous topics, including economic activities, labor and wages, population, transportation, tourism, housing, and education.

1997-01-01

159

Aviation Safety Issues Database  

NASA Technical Reports Server (NTRS)

The aviation safety issues database was instrumental in the refinement and substantiation of the National Aviation Safety Strategic Plan (NASSP). The issues database is a comprehensive set of issues from an extremely broad base of aviation functions, personnel, and vehicle categories, both nationally and internationally. Several aviation safety stakeholders such as the Commercial Aviation Safety Team (CAST) have already used the database. This broader interest was the genesis to making the database publically accessible and writing this report.

Morello, Samuel A.; Ricks, Wendell R.

2009-01-01

160

FLAGdb\\/FST: a database of mapped flanking insertion sites (FSTs) of Arabidopsis thaliana T-DNA transformants  

Microsoft Academic Search

A large collection of T-DNA insertion transformants of Arabidopsis thaliana has been generated at the Institute of Agronomic Research, Versailles, France. The molecular characterisation of the insertion sites is currently performed by sequencing genomic regions flanking the inserted T-DNA (FST). The almost complete sequence of the nuclear genome of A.thaliana provides the framework for organising FSTs in a genome oriented

Franck Samson; Véronique Brunaud; Sandrine Balzergue; B. Dubreucq; L. Lepiniec; G. Pelletier; Michel Caboche; Alain Lecharny

2002-01-01

161

Expanding the forensic German mitochondrial DNA control region database: genetic diversity as a function of sample size and microgeography  

Microsoft Academic Search

Mitochondrial DNA control region sequences were determined in 109 unrelated German Caucasoid individuals from north west\\u000a Germany for both hypervariable regions 1 (HV1) and 2 (HV2) and 100 polymorphic nucleotide positions (nps) were found, 63 in\\u000a HV1 and 37 in HV2. A total of 100 different mtDNA lineages was revealed, of which 7 were shared by 2 individuals and 1

H. Pfeiffer; B. Brinkmann; J. Hühne; B. Rolf; A. A. Morris; R. Steighner; M. M. Holland; P. Forster

1999-01-01

162

Eukaryotic genome size databases  

PubMed Central

Three independent databases of eukaryotic genome size information have been launched or re-released in updated form since 2005: the Plant DNA C-values Database (), the Animal Genome Size Database () and the Fungal Genome Size Database (). In total, these databases provide freely accessible genome size data for >10 000 species of eukaryotes assembled from more than 50 years' worth of literature. Such data are of significant importance to the genomics and broader scientific community as fundamental features of genome structure, for genomics-based comparative biodiversity studies, and as direct estimators of the cost of complete sequencing programs. PMID:17090588

Gregory, T. Ryan; Nicol, James A.; Tamm, Heidi; Kullman, Bellis; Kullman, Kaur; Leitch, Ilia J.; Murray, Brian G.; Kapraun, Donald F.; Greilhuber, Johann; Bennett, Michael D.

2007-01-01

163

Database of Gene Co-Regulation (dGCR): A Web Tool for Analysing Patterns of Gene Co-regulation across Publicly Available Expression Data.  

PubMed

The database of Gene Co-Regulation (dGCR) is a web tool for the analysis of gene relationships based on correlated patterns of gene expression over publicly available transcriptional data. The motivation behind dGCR is that genes whose expression patterns correlate across many experiments tend to be co-regulated and hence share biological function. In addition to revealing functional connections between individual gene pairs, extended sets of co-regulated genes can also be assessed for enrichment of gene ontology classes and interaction pathways. This functionality provides an insight into the biological function of the query gene itself. The dGCR web tool extends the range of expression data curated by existing co-regulation databases and provides additional insights into gene function through the analysis of pathways, gene ontology classes and co-regulation modules. PMID:25628763

Williams, Gareth

2015-01-01

164

Database of Gene Co-Regulation (dGCR): A Web Tool for Analysing Patterns of Gene Co-regulation across Publicly Available Expression Data  

PubMed Central

The database of Gene Co-Regulation (dGCR) is a web tool for the analysis of gene relationships based on correlated patterns of gene expression over publicly available transcriptional data. The motivation behind dGCR is that genes whose expression patterns correlate across many experiments tend to be co-regulated and hence share biological function. In addition to revealing functional connections between individual gene pairs, extended sets of co-regulated genes can also be assessed for enrichment of gene ontology classes and interaction pathways. This functionality provides an insight into the biological function of the query gene itself. The dGCR web tool extends the range of expression data curated by existing co-regulation databases and provides additional insights into gene function through the analysis of pathways, gene ontology classes and co-regulation modules.

Williams, Gareth

2015-01-01

165

DATARIs: Database on Research Institutes  

NSDL National Science Digital Library

The United Nations Institute for Disarmament Research (UNIDIR), in cooperation with the Stockholm International Peace Research Institute (SIPRI), maintain DATARIs, a collection of databases providing information from and about research institutes specializing in international relations and security. DATARIs includes directory databases on research institutes and documentation centers, bibliographic databases on research institute projects and publications, and a database providing information about databases maintained by associated research institutes. Each searchable database offers an easy-to-use search form interface, facilitating queries for users.

166

Development of a DNA microarray to detect antimicrobial resistance genes identified in the national center for biotechnology information database  

Technology Transfer Automated Retrieval System (TEKTRAN)

High density genotyping techniques are needed for investigating antimicrobial resistance especially in the case of multi-drug resistant (MDR) isolates. To achieve this all antimicrobial resistance genes in the NCBI Genbank database were identified by key word searches of sequence annotations and the...

167

The Zoonoses Database-A HyperCard™ Stack on the Macintosh™ Computer for Teaching Veterinary Epidemiology and Public Health  

PubMed Central

For the past 2 years second-year veterinary students have used a HyperCard-based Zoonoses Database to abstract, store and retrieve information on zoonotic diseases. Each student was required to review the veterinary literature for information about one zoonotic disease and enter the information into a HyperCard template which summarized epidemiologic aspects of the disease. A total of 99 diseases are included in the Zoonoses Database. To use this resource in problem-solving, students formed mock 2 to 6 person veterinary practices. Student “practice groups” were then assigned one of 24 case histories and asked to form a rule-out list, select the most probable disease, and provide advice to the client regarding the zoonotic potential of the disease in question. We will continue to expand the database and link life cycles to it.

Hungerford, Laura L.; Smith, Ronald P.; Smith, Ronald D.

1990-01-01

168

The ICRP Database of Dose Coefficients: Workers and Members of the Public, version 1.0 - an extension of ICRP Publications 68 and 72.  

SciTech Connect

A CD-ROM database that gives dose coefficients for inhalation and ingestion of over 800 radionuclides of 91 elements. Inhalation dose coefficients are provided for ten aerosol sizes from 0.001um to 10 um AMAD. Effective dose and equivalent dose coefficients are given for ten integration periods from 1 d to 70y.

Vargo, George J.(BATTELLE (PACIFIC NW LAB)) [BATTELLE (PACIFIC NW LAB)

2000-03-01

169

Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools  

PubMed Central

The non-B DB, available at http://nonb.abcc.ncifcrf.gov, catalogs predicted non-B DNA-forming sequence motifs, including Z-DNA, G-quadruplex, A-phased repeats, inverted repeats, mirror repeats, direct repeats and their corresponding subsets: cruciforms, triplexes and slipped structures, in several genomes. Version 2.0 of the database revises and re-implements the motif discovery algorithms to better align with accepted definitions and thresholds for motifs, expands the non-B DNA-forming motifs coverage by including short tandem repeats and adds key visualization tools to compare motif locations relative to other genomic annotations. Non-B DB v2.0 extends the ability for comparative genomics by including re-annotation of the five organisms reported in non-B DB v1.0, human, chimpanzee, dog, macaque and mouse, and adds seven additional organisms: orangutan, rat, cow, pig, horse, platypus and Arabidopsis thaliana. Additionally, the non-B DB v2.0 provides an overall improved graphical user interface and faster query performance. PMID:23125372

Cer, Regina Z.; Donohue, Duncan E.; Mudunuri, Uma S.; Temiz, Nuri A.; Loss, Michael A.; Starner, Nathan J.; Halusa, Goran N.; Volfovsky, Natalia; Yi, Ming; Luke, Brian T.; Bacolla, Albino; Collins, Jack R.; Stephens, Robert M.

2013-01-01

170

Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools.  

PubMed

The non-B DB, available at http://nonb.abcc.ncifcrf.gov, catalogs predicted non-B DNA-forming sequence motifs, including Z-DNA, G-quadruplex, A-phased repeats, inverted repeats, mirror repeats, direct repeats and their corresponding subsets: cruciforms, triplexes and slipped structures, in several genomes. Version 2.0 of the database revises and re-implements the motif discovery algorithms to better align with accepted definitions and thresholds for motifs, expands the non-B DNA-forming motifs coverage by including short tandem repeats and adds key visualization tools to compare motif locations relative to other genomic annotations. Non-B DB v2.0 extends the ability for comparative genomics by including re-annotation of the five organisms reported in non-B DB v1.0, human, chimpanzee, dog, macaque and mouse, and adds seven additional organisms: orangutan, rat, cow, pig, horse, platypus and Arabidopsis thaliana. Additionally, the non-B DB v2.0 provides an overall improved graphical user interface and faster query performance. PMID:23125372

Cer, Regina Z; Donohue, Duncan E; Mudunuri, Uma S; Temiz, Nuri A; Loss, Michael A; Starner, Nathan J; Halusa, Goran N; Volfovsky, Natalia; Yi, Ming; Luke, Brian T; Bacolla, Albino; Collins, Jack R; Stephens, Robert M

2013-01-01

171

The creation of a public database of precision phantoms to facilitate the evaluation and standardization of advanced visualization and quantification software  

NASA Astrophysics Data System (ADS)

In order to validate CT imaging as a biomarker, it is important to ascertain the variability and artifacts associated with various forms of advanced visualization and quantification software. The purpose of the paper is to describe the rationale behind the creation of a free, public resource that contains phantom datasets for CT designed to facilitate testing, development and standardization of advanced visualization and quantification software. For our research, three phantoms were scanned at multiple kVp and mAs settings utilizing a 64-channel MDCT scanner at a collimation of 0.75 mm. Images were reconstructed at a slice thickness of 0.75 mm and archived in DICOM format. The phantoms consisted of precision spheres, balls of different materials and sizes, and slabs of Last-A-Foam(R) at varying densities. The database of scans is stored in an archive utilizing software developed for the National Cancer Imaging Archive and is publically available. The scans were completed successfully and the datasets are available for free and unrestricted download. The CT images can be accessed in DICOM format via http or FTP or utilizing caGRID. A DICOM database of phantom data was successfully created and made available to the public. We anticipate that this database will be useful as a reference for physicists for quality control purposes, for developers of advanced visualization and quantification software, and for others who need to test the performance of their systems against a known "gold" standard. We plan to add more phantom images in the future and expand to other imaging modalities.

Chen, Joseph J.; Saenz, Naomi J.; Siegel, Eliot L.

2009-02-01

172

DNA  

NSDL National Science Digital Library

In this activity, students extract DNA from their cheek cells and relate the steps in the procedure to the characteristics of cells and biological molecules. Students learn key concepts about the function of DNA during the intervals required for the extraction procedure. A second optional section develops student understanding of the fundamentals of DNA structure, function and replication; this section includes hands-on modeling of DNA replication. This activity, together with our activity, "From Gene to Protein - Transcription and Translation", can be used to teach the basic concepts of molecular biology.

Doherty, Jennifer; Waldron, Ingrid

173

Morchella MLST database  

Technology Transfer Automated Retrieval System (TEKTRAN)

Welcome to the Morchella MLST database. This dedicated database was set up at the CBS-KNAW Biodiversity Center by Vincent Robert in February 2012, using BioloMICS software (Robert et al., 2011), to facilitate DNA sequence-based identifications of Morchella species via the Internet. The current datab...

174

THE COMPILATION OF A PUBLIC DOMAIN DATABASE ON NUCLEAR FUEL PERFORMANCE FOR THE PURPOSE OF CODE DEVELOPMENT AND VALIDATION  

Microsoft Academic Search

This paper describes the compilation of a database on nuclear fuel performance for the purpose of code development and validation. The paper begins with the background behind its formation and the progress made to date in assembling 291 datasets from various sources encompassing PWR, BWR and WWER reactor systems. Agreement has been reached for the inclusion of further cases which

P. M. Chantoin; E. Sartori; J. A. Turnbull

175

Ovarian Kaleidoscope database: ten years and beyond.  

PubMed

Ovarian Kaleidoscope database (OKdb) is an online, searchable, public database containing text-based and DNA microarray data to facilitate research by ovarian researchers. Using key words and predetermined categories, users can search ovarian gene information based on gene function, cell type of expression, cellular localization, hormonal regulation, mutant phenotypes, chromosomal location, ligand-receptor relationship, and other criteria, either alone or in combination. For individual genes, users can access more than 10 extensive DNA microarray datasets to interrogate gene expression patterns in a development-specific and cell type-specific manner. All ligand and receptor genes expressed in the ovary are matched to facilitate investigation of paracrine/autocrine signaling. More than 3500 ovarian genes in the database are matched to 185 gene pathways in the Kyoto Encyclopedia of Genes and Genomes to allow for elucidation of gene interactions and relationships. In addition to >400 genes with infertility or subfertility phenotypes when mutated in mice or humans, the OKdb also lists ~50 and ~40 genes associated with polycystic ovarian syndrome and primary ovarian insufficiency, respectively. The expanding OKdb is updated weekly and allows submission of new genes by ovarian researchers to allow instant access to DNA microarray datasets for newly submitted genes. The present database is a virtual community for ovarian researchers and allows users to instantaneously provide their comments for individual gene pages based on an automated Web-discussion system. In the coming years, we will continue to add new features to serve the ovarian research community. PMID:22441797

Hsueh, Aaron J; Rauch, Rami

2012-06-01

176

DNA.  

ERIC Educational Resources Information Center

Structural form, bonding scheme, and chromatin structure of and gene-modification experiments with deoxyribonucleic acid (DNA) are described. Indicates that DNA's double helix is variable and also flexible as it interacts with regulatory and other molecules to transfer hereditary messages. (DH)

Felsenfeld, Gary

1985-01-01

177

The ICRP database of dose coefficients: Workers and members of the public, version 1.0, an extension of ICRP publications 68 and 72  

Microsoft Academic Search

A CDROM database that gives dose coefficients for inhalation and ingestion of over 800 radionuclides of 91 elements. Inhalation dose coefficients are provided for ten aerosol sizes from 0.001 μm to 10 μm AMAD. Effective dose and equivalent dose coefficients are given for ten integration periods form 1 d to 70 y. Extensive help files summarizing the biokinetic models in

George J. Vargo; George J

2000-01-01

178

Cardiac CT and MRI for congenital heart disease in Asian countries: recent trends in publication based on a scientific database.  

PubMed

In the past 12 years, during the process of imaging congenital heart disease (CHD), Asian doctors have not only made every effort to adhere to established magnetic resonance imaging (MRI) protocols as in Western countries, but also have developed Computed tomography (CT) as an alternative problem-solving technique. Databases have shown that Asian doctors were more inclined to utilize CT than MRI in evaluating CHD. Articles in the literature focusing on CT have been cited more frequently than articles on MRI. Additionally, several repeatedly cited CT articles have become seminal papers in this field. The database reflects a trend suggesting that Asian doctors actively adapt to new techniques and flexibly develop unique strategies to overcome limitations caused by the relatively limited resources often available to them. PMID:23344910

Tsai, I-Chen; Goo, Hyun Woo

2013-06-01

179

The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data.  

PubMed

Substantial new features have been implemented at the Ribosomal Database Project in response to the increased importance of high-throughput rRNA sequence analysis in microbial ecology and related disciplines. The most important changes include quality analysis, including chimera detection, for all available rRNA sequences and the introduction of myRDP Space, a new web component designed to help researchers place their own data in context with the RDP's data. In addition, new video tutorials describe how to use RDP features. Details about RDP data and analytical functions can be found at the RDP-II website (http://rdp.cme.msu.edu/). PMID:17090583

Cole, J R; Chai, B; Farris, R J; Wang, Q; Kulam-Syed-Mohideen, A S; McGarrell, D M; Bandela, A M; Cardenas, E; Garrity, G M; Tiedje, J M

2007-01-01

180

The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data  

PubMed Central

Substantial new features have been implemented at the Ribosomal Database Project in response to the increased importance of high-throughput rRNA sequence analysis in microbial ecology and related disciplines. The most important changes include quality analysis, including chimera detection, for all available rRNA sequences and the introduction of myRDP Space, a new web component designed to help researchers place their own data in context with the RDP's data. In addition, new video tutorials describe how to use RDP features. Details about RDP data and analytical functions can be found at the RDP-II website (). PMID:17090583

Cole, J. R.; Chai, B.; Farris, R. J.; Wang, Q.; Kulam-Syed-Mohideen, A. S.; McGarrell, D. M.; Bandela, A. M.; Cardenas, E.; Garrity, G. M.; Tiedje, J. M.

2007-01-01

181

Ionic Liquids Database- (ILThermo)  

National Institute of Standards and Technology Data Gateway

SRD 147 Ionic Liquids Database- (ILThermo) (Web, free access)   IUPAC Ionic Liquids Database, ILThermo, is a free web research tool that allows users worldwide to access an up-to-date data collection from the publications on experimental investigations of thermodynamic, and transport properties of ionic liquids as well as binary and ternary mixtures containing ionic liquids.

182

ii The query may not be an exact match or even partial match with any data in the database, but since DNA annealing a nity methods work  

E-print Network

-coated paramagnetic beads and the a nity separation operates on another set of single stranded DNA which anneal, etc. 1 Introduction 1.1 Recombinant DNA Technology DNA as a Storage Media. Recall that DNA is a linear at concentrations of about 5 grams of DNA per liter of water. Recombinant DNA Technology. Biotechnological methods

Reif, John H.

183

DNA  

ERIC Educational Resources Information Center

This history for molecular genetics and its explanation of DNA begins with an analysis of the Golden Jubilee essay papers, 1955. The paper ends stating that the higher nervous system is the one major frontier of biological inquiry which still offers some romance of research. (Author/VW)

Stent, Gunther S.

1970-01-01

184

Using data from the public project, Craig VenterSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

Interviewee: Craig Venter DNAi Location:Genome>the project>players>private project Using data from the public project Craig Venter, leader of the private effort at Celera Genomics, speaks about his company's reliance on the public data for reassembly of the Celera sequence.

2008-10-06

185

The PNNL Quantitative Infrared Database for Gas-Phase Sensing: A spectral Library for Environmental, Hazmat, and Public Safety Standoff Detection  

SciTech Connect

Pacific Northwest National Laboratory (PNNL) continues to expand its library of quantitative infrared reference spectra for remote sensing. The gas-phase data are recorded at 0.1 cm-1 resolution, with nitrogen pressure broadening to one atmosphere to emulate spectra recorded in the field. It is planned that the PNNL library will consist of approximately 500 vapor-phase spectra associated with the U.S. Department of Energy's environmental, energy, and public safety missions. At present, the database is comprised of approximately 300 infrared spectra, many of which represent highly reactive or toxic species. For the 298 K data, each reported spectrum is in fact a composite spectrum generated by a Beer's law plot (at each wavelength) to typically 12 measured spectra. Recent additions to the database include the vapors of several semi-volatile and non-volatile liquids using an improved dissemination technique for vaporizing the liquid into the nitrogen carrier gas. Experimental and analytical methods are used to remove several known and new artifacts associated with FTIR gas-phase spectroscopy. Details concerning sample preparation and composite spectrum generation are discussed.

Johnson, Timothy J.; Sams, Robert L.; Sharpe, Steven W.; Arthur J. Sedlacek III, Richard Colton, Tuan Vo-Dinh

2004-03-25

186

TOMATO EXPRESSION DATABASE (TED): A SUITE OF DATA PRESENTATION AND ANALYSIS TOOLS  

Technology Transfer Automated Retrieval System (TEKTRAN)

The Tomato Expression Database (TED) includes three integrated components. The Tomato Microarray Data Warehouse serves as a central repository for raw gene expression data derived from the public tomato cDNA microarray. In addition to expression data, TED stores experimental design and array informa...

187

ESTuber db: an online database for Tuber borchii EST sequences  

Microsoft Academic Search

BACKGROUND: The ESTuber database (http:\\/\\/www.itb.cnr.it\\/estuber) includes 3,271 Tuber borchii expressed sequence tags (EST). The dataset consists of 2,389 sequences from an in-house prepared cDNA library from truffle vegetative hyphae, and 882 sequences downloaded from GenBank and representing four libraries from white truffle mycelia and ascocarps at different developmental stages. An automated pipeline was prepared to process EST sequences using public

Barbara Lazzari; Andrea Caprera; Cristian Cosentino; Alessandra Stella; Luciano Milanesi; Angelo Viotti

2007-01-01

188

Public concern over genetic manipulation, Alexander CapronSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

Alexander Capron DNAi Location:Manipulation>Revolution>players>The controversy The Frankenstein factor Alexander Capron, a lawyer and specialist in bioethics, talks about how fear of Frankenstein captured the public fancy.

2008-10-06

189

Rainfall Simulation Database  

NSDL National Science Digital Library

The British Geomorphological Research Group maintains this rainfall simulation database site. The database includes information about rainfall simulators, as well as their set-up and use. Currently, the database is divided into laboratory, field, and dual-purpose (lab and field) rainfall simulators. For each simulator in the database, users will find information on: "Simulator identification; Contact information; Specification of simulator; performance of simulator; Table of intensities and rainfall characteristics; Costs; Summary of research conducted using the simulator; Publications; and Additional comments." A section on simulation calibration is planned, and a form is provided for those wishing to contribute simulators to the database. A lengthy selection of related references adds to the utility of the database.

190

Wound Healing & Management Node: Titles list Version 1 1 July 2010 Publication list of Evidence Summary titles available in the Wound Healing and Management Node of the JBI COnNECT+ database as at 31 December 2011.  

E-print Network

Wound Healing & Management Node: Titles list Version 1 1 July 2010 Publication list of Evidence Summary titles available in the Wound Healing and Management Node of the JBI COnNECT+ database as at 31 December 2011. Authors: The Wound Healing and Management Node Group This list is updated quarterly Evidence

191

Transforming "The People" into "The Public": The DNA of Community Collaboration.  

ERIC Educational Resources Information Center

This paper examines the development of the concept of the "public" and the "people" in U.S. society. Community problem-solving is an art, and like the art of dance or the game of soccer, the dispositions and skills of communal life are learned by doing and reflecting on what has been done. This essay discusses the "arts" of democracy, including:…

Jack, Elkin Terry

192

Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database  

SciTech Connect

HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms; (2) compared PPP reference specimens of human serum and EDTA, heparin, and citrate-anticoagulated plasma; and (3) created a publicly-available knowledge base (www.bioinformatics. med.umich.edu/hupo/ppp; www.ebi.ac.uk/pride). Thirty-five participating laboratories in 13 countries submitted datasets. Working groups addressed (a) specimen stability and protein concentrations; (b) protein identifications from 18 MS/MS datasets; (c) independent analyses from raw MS-MS spectra; (d) search engine performance, subproteome analyses, and biological insights; (e) antibody arrays; and (f) direct MS/SELDI analyses. MS-MS datasets had 15 710 different International Protein Index (IPI) protein IDs; our integration algorithm applied to multiple matches of peptide sequences yielded 9504 IPI proteins identified with one or more peptides and 3020 proteins identified with two or more peptides (the Core Dataset). These proteins have been characterized with Gene Ontology, InterPro, Novartis Atlas, OMIM, and immunoassay based concentration determinations. The database permits examination of many other subsets, such as 1274 proteins identified with three or more peptides. Reverse protein to DNA matching identified proteins for 118 previously unidentified ORFs. We recommend use of plasma instead of serum, with EDTA (or citrate) for anticoagulation. To improve resolution, sensitivity and reproducibility of peptide identifications and protein matches, we recommend combinations of depletion, fractionation, and MS/MS technologies, with explicit criteria for evaluation of spectra, use of search algorithms, and integration of homologous protein matches. This Special Issue of PROTEOMICS presents papers integral to the collaborative analysis plus many reports of supplementary work on various aspects of the PPP workplan. These PPP results on complexity, dynamic range, incomplete sampling, false-positive matches, and integration of diverse datasets for plasma and serum proteins lay a foundation for development and validation of circulating protein biomarkers in health and disease.

Omenn, Gilbert; States, David J.; Adamski, Marcin; Blackwell, Thomas W.; Menon, Rajasree; Hermjakob, Henning; Apweiler, Rolf; Haab, Brian B.; Simpson, Richard; Eddes, James; Kapp, Eugene; Moritz, Rod; Chan, Daniel W.; Rai, Alex J.; Admon, Arie; Aebersold, Ruedi; Eng, Jimmy K.; Hancock, William S.; Hefta, Stanley A.; Meyer, Helmut; Paik, Young-Ki; Yoo, Jong-Shin; Ping, Peipei; Pounds, Joel G.; Adkins, Joshua N.; Qian, Xiaohong; Wang, Rong; Wasinger, Valerie; Wu, Chi Yue; Zhao, Xiaohang; Zeng, Rong; Archakov, Alexander; Tsugita, Akira; Beer, Ilan; Pandey, Akhilesh; Pisano, Michael; Andrews, Philip; Tammen, Harald; Speicher, David W.; Hanash, Samir M.

2005-08-13

193

Buffmap Database  

NSDL National Science Digital Library

The Institut National de Recherche Agronomique (France) provides online databases of genomes for several organisms, including Buffalo. The database is updated as more data become available, and provide records on loci, genes, microsatellites, polymorphisms, probes, enzymes, homologue loci, alleles, primers, references, and links to external databases. Instructions for submitting data to the databases are provided on-site.

194

The Hawaiian Algal Database: a laboratory LIMS and online resource for biodiversity data  

PubMed Central

Background Organization and presentation of biodiversity data is greatly facilitated by databases that are specially designed to allow easy data entry and organized data display. Such databases also have the capacity to serve as Laboratory Information Management Systems (LIMS). The Hawaiian Algal Database was designed to showcase specimens collected from the Hawaiian Archipelago, enabling users around the world to compare their specimens with our photographs and DNA sequence data, and to provide lab personnel with an organizational tool for storing various biodiversity data types. Description We describe the Hawaiian Algal Database, a comprehensive and searchable database containing photographs and micrographs, geo-referenced collecting information, taxonomic checklists and standardized DNA sequence data. All data for individual samples are linked through unique accession numbers. Users can search online for sample information by accession number, numerous levels of taxonomy, or collection site. At the present time the database contains data representing over 2,000 samples of marine, freshwater and terrestrial algae from the Hawaiian Archipelago. These samples are primarily red algae, although other taxa are being added. Conclusion The Hawaiian Algal Database is a digital repository for Hawaiian algal samples and acts as a LIMS for the laboratory. Users can make use of the online search tool to view and download specimen photographs and micrographs, DNA sequences and relevant habitat data, including georeferenced collecting locations. It is publicly available at . PMID:19728892

Wang, Norman; Sherwood, Alison R; Kurihara, Akira; Conklin, Kimberly Y; Sauvage, Thomas; Presting, Gernot G

2009-01-01

195

Method and system for normalizing biometric variations to authenticate users from a public database and that ensures individual biometric data privacy  

DOEpatents

A password system comprises a set of codewords spaced apart from one another by a Hamming distance (HD) that exceeds twice the variability that can be projected for a series of biometric measurements for a particular individual and that is less than the HD that can be encountered between two individuals. To enroll an individual, a biometric measurement is taken and exclusive-ORed with a random codeword to produce a "reference value." To verify the individual later, a biometric measurement is taken and exclusive-ORed with the reference value to reproduce the original random codeword or its approximation. If the reproduced value is not a codeword, the nearest codeword to it is found, and the bits that were corrected to produce the codeword to it is found, and the bits that were corrected to produce the codeword are also toggled in the biometric measurement taken and the codeword generated during enrollment. The correction scheme can be implemented by any conventional error correction code such as Reed-Muller code R(m,n). In the implementation using a hand geometry device an R(2,5) code has been used in this invention. Such codeword and biometric measurement can then be used to see if the individual is an authorized user. Conventional Diffie-Hellman public key encryption schemes and hashing procedures can then be used to secure the communications lines carrying the biometric information and to secure the database of authorized users.

Strait, Robert S. (Oakland, CA); Pearson, Peter K. (Livermore, CA); Sengupta, Sailes K. (Livermore, CA)

2000-01-01

196

Computational tools and resources for metabolism-related property predictions. 1. Overview of publicly available (free and commercial) databases and software  

PubMed Central

Metabolism has been identified as a defining factor in drug development success or failure because of its impact on many aspects of drug pharmacology, including bioavailability, half-life and toxicity. In this article, we provide an outline and descriptions of the resources for metabolism-related property predictions that are currently either freely or commercially available to the public. These resources include databases with data on, and software for prediction of, several end points: metabolite formation, sites of metabolic transformation, binding to metabolizing enzymes and metabolic stability. We attempt to place each tool in historical context and describe, wherever possible, the data it was based on. For predictions of interactions with metabolizing enzymes, we show a typical set of results for a small test set of compounds. Our aim is to give a clear overview of the areas and aspects of metabolism prediction in which the currently available resources are useful and accurate, and the areas in which they are inadequate or missing entirely. PMID:23088273

Peach, Megan L; Zakharov, Alexey V; Liu, Ruifeng; Pugliese, Angelo; Tawa, Gregory; Wallqvist, Anders; Nicklaus, Marc C

2014-01-01

197

The EMBL nucleotide sequence database  

Microsoft Academic Search

The EMBL Nucleotide Sequence Database (http:\\/\\/ www.ebi.ac.uk\\/embl\\/) is maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data Bank of Japan (DDBJ) and GenBank at the NCBI (USA). Data is exchanged amongst the collaborating databases on a daily basis. The major contributors to the EMBL database are individual authors and genome project groups. Webin is

Guenter Stoesser; Wendy Baker; Alexandra Van Den Broek; Evelyn Camon; Maria Garcia-pastor; Carola Kanz; Tamara Kulikova; Vincent Lombard; Rodrigo Lopez; Helen E. Parkinson; Nicole Redaschi; Peter Sterk; Peter Stoehr; Mary Ann Tuli

2001-01-01

198

DATABASE AUTHENTICATION BY DISTORTION FREE WATERMARKING  

E-print Network

DATABASE AUTHENTICATION BY DISTORTION FREE WATERMARKING Sukriti Bhattacharya and Agostino Cortesi@dsi.unive.it, cortesi@unive.it Keywords: Database watermarking, ZAW, Public key watermark, Abstract interpretation the verification of integrity of the relational databases by using a public zero distortion authentication

Cortesi, Tino

199

Database of Zeolite Structures  

NSDL National Science Digital Library

The Database of Zeolite Structures is provided by the Structure Commission of the International Zeolite Association. Links include an Atlas of Zeolite Framework Types, Collection of Simulated XRD Powder Patterns for Zeolites, Catalog of Disordered Zeolite Structures, Schemes for Building Zeolite Framework Models, and Zeolite Structure References, as well as various publications. The database can be searched or browsed, and contains several useful tools such as the "input your data" link, which allows the user to enter crystallographic data not available in the database and generate the diffraction pattern.

200

Transboundary Freshwater Dispute Database  

NSDL National Science Digital Library

This collection of databases is intended to aid in the assessment of the process of water conflict prevention and resolution. The searchable collections include data such as case studies, freshwater treaties from 1820 to 2001, events concerning historical water relations from 1948 to 1999, a register of international river basins, and information on interstate water compacts in the United States. There is also spatial data on transboundary freshwater indicator variables, international river basins, and a map and image gallery. Other materials include links to the organization's publications and research projects, and a set of links to other databases and publications on freshwater conflict issues.

201

FACILITY DATABASE  

Cancer.gov

January 2008 LASP FACILTY Database Form 5.000 Issue Reporting Form This form is used to report data and/or program related issues regarding the FACILITY database, Supplemental, or the LASP Online Access System. Before submitting this form,

202

Biofuel Database  

National Institute of Standards and Technology Data Gateway

Biofuel Database (Web, free access)   This database brings together structural, biological, and thermodynamic data for enzymes that are either in current use or are being considered for use in the production of biofuels.

203

Prediction of cis-QTLs in a pair of inbred mouse strains with the use of expression and haplotype data from public databases.  

PubMed

Cis-QTLs are important candidates for any other trait that maps to the same locus. In this article we have used publicly available databases and a small microarray data set to "map" cis-QTLs in the ILS and ISS inbred mouse strains without the need to generate microarray data from an ILSXISS segregating population. Expression data were obtained from brains of C57BL/6, DBA/2, ILS, and ISS. Cis-QTLs were mapped for the 760 transcripts found to be differentially expressed between the C57BL/6 and DBA/2 using expression data previously obtained from the BXD RIs. The 469 detected cis-QTLs were then examined for SNP haplotypes and expression patterns that could relate the ILS and ISS to the C57BL/6 and DBA/2. Of the 338 cis-QTL transcripts that had informative haplotypes, 189 were significantly different between the ILS and ISS with 184 showing segregation of haplotype with expression. These were considered to be probable cis-QTLs in the ILS and ISS. There were almost certainly additional ILS/ISS cis-QTLs among the other transcripts with informative haplotypes, but in the absence of an ILS/ISS expression difference, the level of confidence was reduced. Several of the putative ILS/ISS cis-QTLs are considered important candidate genes because they are linked to ILS/ISS behavioral QTLs. A potential ascertainment bias related to strain-dependent target sequences was observed suggesting that as much as 35% of the cis-QTLs were hybridization artifacts. Nonetheless, the results suggest that this approach is an economical and widely applicable method for mapping cis-QTLs in a strain pair of interest. PMID:16783643

Radcliffe, Richard A; Lee, Michael J; Williams, Robert W

2006-06-01

204

Database Administrator  

ERIC Educational Resources Information Center

The Internet and electronic commerce (e-commerce) generate lots of data. Data must be stored, organized, and managed. Database administrators, or DBAs, work with database software to find ways to do this. They identify user needs, set up computer databases, and test systems. They ensure that systems perform as they should and add people to the…

Moore, Pam

2010-01-01

205

Computer Note A Prototype Object Database for  

E-print Network

Computer Note A Prototype Object Database for Mitochondrial DNA Variation J. E. NEIGEL AND P preserved. We hope to prevent further loss by establishing a community database for population genetic surveys. We explored the feasibility of a population genetics database by developing a prototype

Neigel, Joseph E.

206

JICST Factual Database(1)  

NASA Astrophysics Data System (ADS)

The outline of JICST factual database (JOIS-F), which JICST has started from January, 1988, and its online service are described in this paper. First, the author mentions the circumstances from 1973, when its planning was started, to the present, and its relation to "Project by Special Coordination Founds for Promoting Science and Technology". Secondly, databases, which are now under development aiming to start its services from fiscal 1988 or fiscal 1989, of DNA, metallic material intensity, crystal structure, chemical substance regulations, and so forth, are described. Lastly, its online service is briefly explained.

Kurosawa, Shinji

207

National Ambient Radiation Database  

SciTech Connect

The U.S. Environmental Protection Agency (EPA) recently developed a searchable database and website for the Environmental Radiation Ambient Monitoring System (ERAMS) data. This site contains nationwide radiation monitoring data for air particulates, precipitation, drinking water, surface water and pasteurized milk. This site provides location-specific as well as national information on environmental radioactivity across several media. It provides high quality data for assessing public exposure and environmental impacts resulting from nuclear emergencies and provides baseline data during routine conditions. The database and website are accessible at www.epa.gov/enviro/. This site contains (1) a query for the general public which is easy to use--limits the amount of information provided, but includes the ability to graph the data with risk benchmarks and (2) a query for a more technical user which allows access to all of the data in the database, (3) background information on ER AMS.

Dziuban, J.; Sears, R.

2003-02-25

208

Fast decision tree-based method to index large DNA-protein sequence databases using hybrid distributed-shared memory programming model.  

PubMed

In recent times, the size of biological databases has increased significantly, with the continuous growth in the number of users and rate of queries; such that some databases have reached the terabyte size. There is therefore, the increasing need to access databases at the fastest rates possible. In this paper, the decision tree indexing model (PDTIM) was parallelised, using a hybrid of distributed and shared memory on resident database; with horizontal and vertical growth through Message Passing Interface (MPI) and POSIX Thread (PThread), to accelerate the index building time. The PDTIM was implemented using 1, 2, 4 and 5 processors on 1, 2, 3 and 4 threads respectively. The results show that the hybrid technique improved the speedup, compared to a sequential version. It could be concluded from results that the proposed PDTIM is appropriate for large data sets, in terms of index building time. PMID:24794073

Jaber, Khalid Mohammad; Abdullah, Rosni; Rashid, Nur'Aini Abdul

2014-01-01

209

The EMBL Nucleotide Sequence Database  

Microsoft Academic Search

The EMBL Nucleotide Sequence Database (http:\\/\\/ www.ebi.ac.uk\\/embl\\/), maintained at the European Bioinformatics Institute (EBI), incorporates, organ- izes and distributes nucleotide sequences from public sources. The database is a part of an inter- national collaboration with DDBJ (Japan) and GenBank (USA). Data are exchanged between the collaborating databases on a daily basis to achieve optimal synchrony. The web-based tool, Webin, is

Tamara Kulikova; Philippe Aldebert; Nicola Althorpe; Wendy Baker; Kirsty Bates; Paul Browne; Alexandra Van Den Broek; Guy Cochrane; Karyn Duggan; Ruth Eberhardt; Nadeem Faruque; Maria Garcia-pastor; Nicola Harte; Carola Kanz; Rasko Leinonen; Quan Lin; Vincent Lombard; Rodrigo Lopez; Renato Mancuso; Michelle Mchale; Francesco Nardone; Ville Silventoinen; Peter Stoehr; Guenter Stoesser; Mary Ann Tuli; Katerina Tzouvara; Robert Vaughan; Dan Wu; Weimin Zhu; Rolf Apweiler

2004-01-01

210

Neogene Mammal Database  

NSDL National Science Digital Library

There are plenty of mammal databases that deal with existing taxonomies and such, but where can one go to find information about land mammal taxa from the Eurasian Miocene to Pleistocene periods? They need look no further than this fine website, which provides access to such material, courtesy of an international advisory board, headed by Mikael Fortelius of the University of Helsinki. First-time visitors may want to look over the data conventions section first. Here they can learn about the proper use of taxonomic fields, and also view such taxonomic examples from the database. Users may also want to look over the browsing section, as it serves as a good orientation to effectively using the database. For those engaged in scholarly endeavors related to the field, there is also a publications section that offers access to recent works that draw on this rather voluminous database.

211

Fun Databases: My Top Ten.  

ERIC Educational Resources Information Center

Provides reviews of 10 online databases: Consumer Reports; Public Opinion Online; Encyclopedia of Associations; Official Airline Guide Adventure Atlas and Events Calendar; CENDATA; Hollywood Hotline; Fearless Taster; Soap Opera Summaries; and Human Sexuality. (LRW)

O'Leary, Mick

1992-01-01

212

IOPI Database of Plant Databases  

NSDL National Science Digital Library

The International Organization for Plant Information (IOPI), a Commission of the International Union of Biological Sciences (IUBS), manages the Database of Plant Databases (DPD). The DPD is a global list of plant databases including Taxonomic databases ("with systematic information on families or genera, or for Flora projects"); Collection catalogs (usually of herbaria); and DELTA datasets (DELTA is "the Description Language for Taxonomy, a data format for character data, used for identification, key construction and the generation of descriptions."). The DPD may be searched using numerous specified fields, or it may be viewed in its entirety -- by Database Name, Host Name, or Host Country. Though bare bones in appearance, this extensive database contains a gold mine of information, with hundreds of hyperlinks to valuable plant databases.

213

Addition of a breeding database in the Genome Database for Rosaceae  

PubMed Central

Breeding programs produce large datasets that require efficient management systems to keep track of performance, pedigree, geographical and image-based data. With the development of DNA-based screening technologies, more breeding programs perform genotyping in addition to phenotyping for performance evaluation. The integration of breeding data with other genomic and genetic data is instrumental for the refinement of marker-assisted breeding tools, enhances genetic understanding of important crop traits and maximizes access and utility by crop breeders and allied scientists. Development of new infrastructure in the Genome Database for Rosaceae (GDR) was designed and implemented to enable secure and efficient storage, management and analysis of large datasets from the Washington State University apple breeding program and subsequently expanded to fit datasets from other Rosaceae breeders. The infrastructure was built using the software Chado and Drupal, making use of the Natural Diversity module to accommodate large-scale phenotypic and genotypic data. Breeders can search accessions within the GDR to identify individuals with specific trait combinations. Results from Search by Parentage lists individuals with parents in common and results from Individual Variety pages link to all data available on each chosen individual including pedigree, phenotypic and genotypic information. Genotypic data are searchable by markers and alleles; results are linked to other pages in the GDR to enable the user to access tools such as GBrowse and CMap. This breeding database provides users with the opportunity to search datasets in a fully targeted manner and retrieve and compare performance data from multiple selections, years and sites, and to output the data needed for variety release publications and patent applications. The breeding database facilitates efficient program management. Storing publicly available breeding data in a database together with genomic and genetic data will further accelerate the cross-utilization of diverse data types by researchers from various disciplines. Database URL: http://www.rosaceae.org/breeders_toolbox PMID:24247530

Evans, Kate; Jung, Sook; Lee, Taein; Brutcher, Lisa; Cho, Ilhyung; Peace, Cameron; Main, Dorrie

2013-01-01

214

Addition of a breeding database in the Genome Database for Rosaceae.  

PubMed

Breeding programs produce large datasets that require efficient management systems to keep track of performance, pedigree, geographical and image-based data. With the development of DNA-based screening technologies, more breeding programs perform genotyping in addition to phenotyping for performance evaluation. The integration of breeding data with other genomic and genetic data is instrumental for the refinement of marker-assisted breeding tools, enhances genetic understanding of important crop traits and maximizes access and utility by crop breeders and allied scientists. Development of new infrastructure in the Genome Database for Rosaceae (GDR) was designed and implemented to enable secure and efficient storage, management and analysis of large datasets from the Washington State University apple breeding program and subsequently expanded to fit datasets from other Rosaceae breeders. The infrastructure was built using the software Chado and Drupal, making use of the Natural Diversity module to accommodate large-scale phenotypic and genotypic data. Breeders can search accessions within the GDR to identify individuals with specific trait combinations. Results from Search by Parentage lists individuals with parents in common and results from Individual Variety pages link to all data available on each chosen individual including pedigree, phenotypic and genotypic information. Genotypic data are searchable by markers and alleles; results are linked to other pages in the GDR to enable the user to access tools such as GBrowse and CMap. This breeding database provides users with the opportunity to search datasets in a fully targeted manner and retrieve and compare performance data from multiple selections, years and sites, and to output the data needed for variety release publications and patent applications. The breeding database facilitates efficient program management. Storing publicly available breeding data in a database together with genomic and genetic data will further accelerate the cross-utilization of diverse data types by researchers from various disciplines. Database URL: http://www.rosaceae.org/breeders_toolbox. PMID:24247530

Evans, Kate; Jung, Sook; Lee, Taein; Brutcher, Lisa; Cho, Ilhyung; Peace, Cameron; Main, Dorrie

2013-01-01

215

Cancer Control Publications 1998-2011: FAQ  

Cancer.gov

CC Publications is a searchable database developed by DCCPS that includes staff, contract investigators, and grantee publications. This database demonstrates the depth and breadth of research publications in cancer control and population sciences funded by NCI.

216

Glycoproteomic and glycomic databases  

PubMed Central

Protein glycosylation serves critical roles in the cellular and biological processes of many organisms. Aberrant glycosylation has been associated with many illnesses such as hereditary and chronic diseases like cancer, cardiovascular diseases, neurological disorders, and immunological disorders. Emerging mass spectrometry (MS) technologies that enable the high-throughput identification of glycoproteins and glycans have accelerated the analysis and made possible the creation of dynamic and expanding databases. Although glycosylation-related databases have been established by many laboratories and institutions, they are not yet widely known in the community. Our study reviews 15 different publicly available databases and identifies their key elements so that users can identify the most applicable platform for their analytical needs. These databases include biological information on the experimentally identified glycans and glycopeptides from various cells and organisms such as human, rat, mouse, fly and zebrafish. The features of these databases - 7 for glycoproteomic data, 6 for glycomic data, and 2 for glycan binding proteins are summarized including the enrichment techniques that are used for glycoproteome and glycan identification. Furthermore databases such as Unipep, GlycoFly, GlycoFish recently established by our group are introduced. The unique features of each database, such as the analytical methods used and bioinformatical tools available are summarized. This information will be a valuable resource for the glycobiology community as it presents the analytical methods and glycosylation related databases together in one compendium. It will also represent a step towards the desired long term goal of integrating the different databases of glycosylation in order to characterize and categorize glycoproteins and glycans better for biomedical research. PMID:24725457

2014-01-01

217

The Molecular Biology Database Collection: 2006 update.  

PubMed

The NAR Molecular Biology Database Collection is a public online resource that contains links to all databases described in this issue of Nucleic Acids Research. In addition, this collection lists databases that have been featured in previous issues of NAR, as well as selected other databases that are freely available to the public and may be useful to the molecular biologist. The 2006 update includes 858 databases, 139 more than the previous one. The databases come with brief summaries, many of which have been updated recently. Each database is assigned a stable accession number that does not change if the database moves to a new location and its URL, authors' names or the contact person address are updated. The complete database list and summaries are available online at the Nucleic Acids Research website http://nar.oxfordjournals.org/. PMID:16381871

Galperin, Michael Y

2006-01-01

218

ASC Publications  

NSDL National Science Digital Library

The University of Wisconsin's Applied Superconductivity Center (ASC) has a publications page with a good selection of online papers on superconductivity. The page contains a searchable publications database, a list of all ASC papers online, and a list of papers supported by the National Science Foundation.

219

Identification of RNA editing sites in the SNP database  

PubMed Central

The relationship between human inherited genomic variations and phenotypic differences has been the focus of much research effort in recent years. These studies benefit from millions of single-nucleotide polymorphism (SNP) records available in public databases, such as dbSNP. The importance of identifying false dbSNP records increases with the growing role played by SNPs in linkage analysis for disease traits. In particular, the emerging understanding of the abundance of DNA and RNA editing calls for a careful distinction between inherited SNPs and somatic DNA and RNA modifications. In order to demonstrate that some of the SNP database records are actually somatic modification, we focus on one type of these modifications, namely A-to-I RNA editing, and present evidence for hundreds of dbSNP records that are actually editing sites. We provide a list of 102 RNA editing sites previously annotated in dbSNP database as SNPs, and experimentally validate seven of these. Interestingly, we show how dbSNP can serve as a starting point to look for new editing sites. Our results, for this particular type of RNA editing, demonstrate the need for a careful analysis of SNP databases in light of the increasing recognition of the significance of somatic sequence modifications. PMID:16100382

Eisenberg, Eli; Adamsky, Konstantin; Cohen, Lital; Amariglio, Ninette; Hirshberg, Abraham; Rechavi, Gideon; Levanon, Erez Y.

2005-01-01

220

DNA polymerases drive DNA sequencing-by-synthesis technologies: both past and present  

PubMed Central

Next-generation sequencing (NGS) technologies have revolutionized modern biological and biomedical research. The engines responsible for this innovation are DNA polymerases; they catalyze the biochemical reaction for deriving template sequence information. In fact, DNA polymerase has been a cornerstone of DNA sequencing from the very beginning. Escherichia coli DNA polymerase I proteolytic (Klenow) fragment was originally utilized in Sanger’s dideoxy chain-terminating DNA sequencing chemistry. From these humble beginnings followed an explosion of organism-specific, genome sequence information accessible via public database. Family A/B DNA polymerases from mesophilic/thermophilic bacteria/archaea were modified and tested in today’s standard capillary electrophoresis (CE) and NGS sequencing platforms. These enzymes were selected for their efficient incorporation of bulky dye-terminator and reversible dye-terminator nucleotides respectively. Third generation, real-time single molecule sequencing platform requires slightly different enzyme properties. Enterobacterial phage ?29 DNA polymerase copies long stretches of DNA and possesses a unique capability to efficiently incorporate terminal phosphate-labeled nucleoside polyphosphates. Furthermore, ?29 enzyme has also been utilized in emerging DNA sequencing technologies including nanopore-, and protein-transistor-based sequencing. DNA polymerase is, and will continue to be, a crucial component of sequencing technologies. PMID:25009536

Chen, Cheng-Yao

2014-01-01

221

NUCLEAR DATABASES FOR REACTOR APPLICATIONS.  

SciTech Connect

The National Nuclear Data Center (NNDC): An overview of nuclear databases, related products, nuclear data Web services and publications. The NNDC collects, evaluates, and disseminates nuclear physics data for basic research and applied nuclear technologies. The NNDC maintains and contributes to the nuclear reaction (ENDF, CSISRS) and nuclear structure databases along with several others databases (CapGam, MIRD, IRDF-2002) and provides coordination for the Cross Section Evaluation Working Group (CSEWG) and the US Nuclear Data Program (USNDP). The Center produces several publications and codes such as Atlas of Neutron Resonances, Nuclear Wallet Cards booklets and develops codes, such as nuclear reaction model code Empire.

PRITYCHENKO, B.; ARCILLA, R.; BURROWS, T.; HERMAN, M.W.; MUGHABGHAB, S.; OBLOZINSKY, P.; ROCHMAN, D.; SONZOGNI, A.A.; TULI, J.; WINCHELL, D.F.

2006-06-05

222

RiceFOX: A Database of Arabidopsis Mutant Lines Overexpressing Rice Full-Length cDNA that Contains a Wide Range of Trait Information to Facilitate Analysis of Gene Function  

PubMed Central

Identification of gene function is important not only for basic research but also for applied science, especially with regard to improvements in crop production. For rapid and efficient elucidation of useful traits, we developed a system named FOX hunting (Full-length cDNA Over-eXpressor gene hunting) using full-length cDNAs (fl-cDNAs). A heterologous expression approach provides a solution for the high-throughput characterization of gene functions in agricultural plant species. Since fl-cDNAs contain all the information of functional mRNAs and proteins, we introduced rice fl-cDNAs into Arabidopsis plants for systematic gain-of-function mutation. We generated >30,000 independent Arabidopsis transgenic lines expressing rice fl-cDNAs (rice FOX Arabidopsis mutant lines). These rice FOX Arabidopsis lines were screened systematically for various criteria such as morphology, photosynthesis, UV resistance, element composition, plant hormone profile, metabolite profile/fingerprinting, bacterial resistance, and heat and salt tolerance. The information obtained from these screenings was compiled into a database named ‘RiceFOX’. This database contains around 18,000 records of rice FOX Arabidopsis lines and allows users to search against all the observed results, ranging from morphological to invisible traits. The number of searchable items is approximately 100; moreover, the rice FOX Arabidopsis lines can be searched by rice and Arabidopsis gene/protein identifiers, sequence similarity to the introduced rice fl-cDNA and traits. The RiceFOX database is available at http://ricefox.psc.riken.jp/. PMID:21186176

Sakurai, Tetsuya; Kondou, Youichi; Akiyama, Kenji; Kurotani, Atsushi; Higuchi, Mieko; Ichikawa, Takanari; Kuroda, Hirofumi; Kusano, Miyako; Mori, Masaki; Saitou, Tsutomu; Sakakibara, Hitoshi; Sugano, Shoji; Suzuki, Makoto; Takahashi, Hideki; Takahashi, Shinya; Takatsuji, Hiroshi; Yokotani, Naoki; Yoshizumi, Takeshi; Saito, Kazuki; Shinozaki, Kazuo; Oda, Kenji; Hirochika, Hirohiko; Matsui, Minami

2011-01-01

223

RiceFOX: a database of Arabidopsis mutant lines overexpressing rice full-length cDNA that contains a wide range of trait information to facilitate analysis of gene function.  

PubMed

Identification of gene function is important not only for basic research but also for applied science, especially with regard to improvements in crop production. For rapid and efficient elucidation of useful traits, we developed a system named FOX hunting (Full-length cDNA Over-eXpressor gene hunting) using full-length cDNAs (fl-cDNAs). A heterologous expression approach provides a solution for the high-throughput characterization of gene functions in agricultural plant species. Since fl-cDNAs contain all the information of functional mRNAs and proteins, we introduced rice fl-cDNAs into Arabidopsis plants for systematic gain-of-function mutation. We generated >30,000 independent Arabidopsis transgenic lines expressing rice fl-cDNAs (rice FOX Arabidopsis mutant lines). These rice FOX Arabidopsis lines were screened systematically for various criteria such as morphology, photosynthesis, UV resistance, element composition, plant hormone profile, metabolite profile/fingerprinting, bacterial resistance, and heat and salt tolerance. The information obtained from these screenings was compiled into a database named 'RiceFOX'. This database contains around 18,000 records of rice FOX Arabidopsis lines and allows users to search against all the observed results, ranging from morphological to invisible traits. The number of searchable items is approximately 100; moreover, the rice FOX Arabidopsis lines can be searched by rice and Arabidopsis gene/protein identifiers, sequence similarity to the introduced rice fl-cDNA and traits. The RiceFOX database is available at http://ricefox.psc.riken.jp/. PMID:21186176

Sakurai, Tetsuya; Kondou, Youichi; Akiyama, Kenji; Kurotani, Atsushi; Higuchi, Mieko; Ichikawa, Takanari; Kuroda, Hirofumi; Kusano, Miyako; Mori, Masaki; Saitou, Tsutomu; Sakakibara, Hitoshi; Sugano, Shoji; Suzuki, Makoto; Takahashi, Hideki; Takahashi, Shinya; Takatsuji, Hiroshi; Yokotani, Naoki; Yoshizumi, Takeshi; Saito, Kazuki; Shinozaki, Kazuo; Oda, Kenji; Hirochika, Hirohiko; Matsui, Minami

2011-02-01

224

Image Databases.  

ERIC Educational Resources Information Center

Different kinds of pictorial databases are described with respect to aims, user groups, search possibilities, storage, and distribution. Some specific examples are given for databases used for the following purposes: (1) labor markets for artists; (2) document management; (3) telling a story; (4) preservation (archives and museums); (5) research;…

Pettersson, Rune

225

Database Manager  

ERIC Educational Resources Information Center

It is normal practice today for organizations to store large quantities of records of related information as computer-based files or databases. Purposeful information is retrieved by performing queries on the data sets. The purpose of DATABASE MANAGER is to communicate to students the method by which the computer performs these queries. This…

Martin, Andrew

2010-01-01

226

A Web Based Document Database  

E-print Network

We describe a document database, developed for BTeV, which has now been adopted for use by other collaborations. A single web based database and archival system is used to maintain public and internal documents as well as documents for a related collaboration. The database performs archiving, versioning, access control, and easy remote access and submission. We cover the technical and security requirements of the database and its implementation. Usage patterns, improvements in our collaborative style, and missteps along the way are also discussed.

E. W. Vaandering

2003-05-27

227

DNA Barcoding  

NSDL National Science Digital Library

This is a two-part animation. Â?DNA Barcoding, Part 1,Â? provides an overview of how DNA barcoding of animals can be used to identify an unknown sample or discover a new species. Cytochrome c oxidase subunit 1 (COI) is found in the mitochondria as part of the electron transport chain. The COI gene is used for DNA barcoding. Just like a barcode on an item in a grocery store identifies a product, a DNA barcode (determined by DNA sequencing) is used to identify species. Part 1 run time: 1 minute, 40 seconds. Â?DNA Barcoding, Part 2Â? details how small tissue samples are used for DNA barcoding, including a review of the laboratory and bioinformatics steps used in barcoding: DNA purification, polymerase chain reaction (PCR), agarose gel electrophoresis, DNA sequencing and analysis, and DNA sequence identification using the Basic Local Alignment Search Tool (BLAST) or the Barcode of Life Database (BOLD). Part 2 run time: 4 minutes, 15 seconds. Animation is closed captioned.

2012-10-22

228

Comparing the public and private sequencing projects, Craig VenterSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

Interviewee: Craig Venter DNAi Location:Genome>the project>players>private project Comparing public and private Craig Venter, the leader of the private genome effort at Celera Genomics, talks about the differences between the public and private approaches.

2008-10-06

229

The Chloroplast Function Database: a large-scale collection of Arabidopsis Ds/Spm- or T-DNA-tagged homozygous lines for nuclear-encoded chloroplast proteins, and their systematic phenotype analysis.  

PubMed

A majority of the proteins of the chloroplast are encoded by the nuclear genome, and are post-translationally targeted to the chloroplast. From databases of tagged insertion lines at international seed stock centers and our own stock, we selected 3246 Ds/Spm (dissociator/suppressor-mutator) transposon- or T-DNA-tagged Arabidopsis lines for genes encoding 1369 chloroplast proteins (about 66% of the 2090 predicted chloroplast proteins) in which insertions disrupt the protein-coding regions. We systematically observed 3-week-old seedlings grown on agar plates, identified mutants with abnormal phenotypes and collected homozygous lines with wild-type phenotypes. We also identified insertion lines for which no homozygous plants were obtained. To date, we have identified 111 lines with reproducible seedling phenotypes, 122 lines for which we could not obtain homozygotes and 1290 homozygous lines without a visible phenotype. The Chloroplast Function Database presents the molecular and phenotypic information obtained from this resource. The database provides tools for searching for mutant lines using Arabidopsis Genome Initiative (AGI) locus numbers, tagged line numbers and phenotypes, and provides rapid access to detailed information on the tagged line resources. Moreover, our collection of insertion homozygotes provides a powerful tool to accelerate the functional analysis of nuclear-encoded chloroplast proteins in Arabidopsis. The Chloroplast Function Database is freely available at http://rarge.psc.riken.jp/chloroplast/. The homozygous lines generated in this project are also available from the various Arabidopsis stock centers. We have donated the insertion homozygotes to their originating seed stock centers. PMID:19912565

Myouga, Fumiyoshi; Akiyama, Kenji; Motohashi, Reiko; Kuromori, Takashi; Ito, Takuya; Iizumi, Haruko; Ryusui, Rie; Sakurai, Tetsuya; Shinozaki, Kazuo

2010-02-01

230

The RIKEN integrated database of mammals  

PubMed Central

The RIKEN integrated database of mammals (http://scinets.org/db/mammal) is the official undertaking to integrate its mammalian databases produced from multiple large-scale programs that have been promoted by the institute. The database integrates not only RIKEN’s original databases, such as FANTOM, the ENU mutagenesis program, the RIKEN Cerebellar Development Transcriptome Database and the Bioresource Database, but also imported data from public databases, such as Ensembl, MGI and biomedical ontologies. Our integrated database has been implemented on the infrastructure of publication medium for databases, termed SciNetS/SciNeS, or the Scientists’ Networking System, where the data and metadata are structured as a semantic web and are downloadable in various standardized formats. The top-level ontology-based implementation of mammal-related data directly integrates the representative knowledge and individual data records in existing databases to ensure advanced cross-database searches and reduced unevenness of the data management operations. Through the development of this database, we propose a novel methodology for the development of standardized comprehensive management of heterogeneous data sets in multiple databases to improve the sustainability, accessibility, utility and publicity of the data of biomedical information. PMID:21076152

Masuya, Hiroshi; Makita, Yuko; Kobayashi, Norio; Nishikata, Koro; Yoshida, Yuko; Mochizuki, Yoshiki; Doi, Koji; Takatsuki, Terue; Waki, Kazunori; Tanaka, Nobuhiko; Ishii, Manabu; Matsushima, Akihiro; Takahashi, Satoshi; Hijikata, Atsushi; Kozaki, Kouji; Furuichi, Teiichi; Kawaji, Hideya; Wakana, Shigeharu; Nakamura, Yukio; Yoshiki, Atsushi; Murata, Takehide; Fukami-Kobayashi, Kaoru; Mohan, Sujatha; Ohara, Osamu; Hayashizaki, Yoshihide; Mizoguchi, Riichiro; Obata, Yuichi; Toyoda, Tetsuro

2011-01-01

231

MUGEN mouse database; animal models of human immunological diseases.  

PubMed

The MUGEN mouse database (MMdb) (www.mugen-noe.org/database/) is a database of murine models of immune processes and immunological diseases. Its aim is to share and publicize information on mouse strain characteristics and availability from participating institutions. MMdb's basic classification of models is based on three major research application categories: Models of Human Disease, Models of Immune Processes and Transgenic Tools. Data on mutant strains includes detailed information on affected gene(s), mutant allele(s) and genetic background (DNA origin, gene targeted, host and backcross strain background). Each gene/transgene index also includes IDs and direct links to Ensembl, ArrayExpress, EURExpress and NCBI's Entrez Gene database. Phenotypic description is standardized and hierarchically structured, based on MGI's mammalian phenotypic ontology terms. Availability (e.g. live mice, cryopreserved embryos, sperm and ES cells) is clearly indicated, along with handling and genotyping details (in the form of documents or hyperlinks) and all relevant contact information (including EMMA and Jax/IMSR hyperlinks where available). MMdb's design offers a user-friendly query interface and provides instant access to the list of mutant strains and genes. Database access is free of charge and there are no registration requirements for data querying. PMID:17932065

Aidinis, V; Chandras, C; Manoloukos, M; Thanassopoulou, A; Kranidioti, K; Armaka, M; Douni, E; Kontoyiannis, D L; Zouberakis, M; Kollias, G

2008-01-01

232

ARTI Refrigerant Database  

SciTech Connect

The Refrigerant Database consolidates and facilitates access to information to assist industry in developing equipment using alternative refrigerants. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air- conditioning and refrigeration equipment. The complete documents are not included, though some may be added at a later date. The database identifies sources of specific information on R-32, R-123, R-124, R- 125, R-134a, R-141b, R142b, R-143a, R-152a, R-290 (propane), R-717 (ammonia), ethers, and others as well as azeotropic and zeotropic blends of these fluids. It addresses polyalkylene glycol (PAG), ester, and other lubricants. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits.

Calm, J.M.

1992-04-30

233

Alcohol Industry & Policy Database  

NSDL National Science Digital Library

The Marin Institute for the Prevention of Alcohol and Other Drug Problems maintains the Alcohol Industry & Policy Database, which contains bibliographic citations and abstracts for more than 13,000 articles and news stories on the alcohol beverage industry, alcohol policy, and the prevention of alcohol-related problems. The citations in the database span from 1991 to the present and are updated monthly. Users may conduct cross-field queries of the database by keywords, subject headings, company name, and publication date. The search facility includes Word Wheels, which are interactive Java applets that help users to identify indexed terms quickly, thereby "eliminat[ing] trial-and-error searching [and] produc[ing] more accurate searches."

Problems., Marin I.

234

Databases and software for the analysis of mutations in the human p53 gene, the human hprt gene and the lacZ gene in transgenic rodents.  

PubMed

We have created databases and software applications for the analysis of DNA mutations in the human p53 gene, the human hprt gene and the rodent transgenic lacZ locus. The databases themselves are stand-alone dBase files and the software for analysis of the databases runs on IBM- compatible computers. The software created for these databases permits filtering, ordering, report generation and display of information in the database. In addition, a significant number of routines have been developed for the analysis of single base substitutions. One method of obtaining the databases and software is via the World Wide Web (WWW). Open home page http://sunsite.unc.edu/dnam/mainpage.ht ml with a WWW browser. Alternatively, the databases and programs are available via public ftp from anonymous@sunsite.unc.edu. There is no password required to enter the system. The databases and software are found in subdirectory pub/academic/biology/dna-mutations. Two other programs are available at the WWW site, a program for comparison of mutational spectra and a program for entry of mutational data into a relational database. PMID:8594557

Cariello, N F; Douglas, G R; Soussi, T

1996-01-01

235

Ant Database  

NSDL National Science Digital Library

Research entomologist Ted Schultz from the Smithsonian Institution maintains this impressive work in progress. This online database represents the Smithsonian's identified ant collection, including 4,580 valid named species or subspecies. The taxonomy is current with Bolton's 1995 catalog and includes reported holdings through June 1998. The database may be queried by Subfamily, Tribe, Genus, Subgenus, Species, Subspecies, Author, or Types, and typical returns give concise taxonomic information, total specimens (workers, females, and males), author, and year.

Schultz, Ted.

2000-01-01

236

Tsunami Database  

NSDL National Science Digital Library

The Tsunami Database is a global digital database containing information on more than 2000 tsunamis maintained by the National Geophysical Data Center. This is an interactive site; the user is asked to enter search parameters such as date, latitude and longitude, cause of the tsunami - earthquake, landslide, volcano, or all combined - magnitude, and death. Information is then generated on tsunamis that match that data. The National Geophysical Data Center also maintains an historic slide set collection of tsunami damage.

237

The Molecular Biology Database Collection: 2005 update.  

PubMed

The Nucleic Acids Research Molecular Biology Database Collection is a public online resource that lists the databases described in this and previous issues of Nucleic Acids Research together with other databases of value to the biologist and available throughout the world. All databases included in this Collection are freely available to the public. The 2005 update includes 719 databases, 171 more than the 2004 one. The databases are organized in a hierarchical classification that simplifies the process of finding the right database for any given task. The growing number of databases related to immunology, plant and organelle research have been accommodated by separating them into three new categories. The database summaries provide brief descriptions of the databases, contact details, appropriate references and acknowledgements. The online summaries also serve as a venue for the maintainers of each database to introduce database updates and other improvements in the scope and tools. These updates are particularly important for those databases that have not been described in print in the recent past. The database list and summaries are available online at the Nucleic Acids Research web site, http://nar.oupjournals.org/. PMID:15608247

Galperin, Michael Y

2005-01-01

238

National Tourism Database  

NSDL National Science Digital Library

Developed by the Michigan State University Extension Tourism Area of Expertise and the National Tourism Education Design Team, this site contains information on numerous resources related to tourism education, including bulletins, research reports, videos, and training programs. Nearly 100 of the documents featured are full-text. Users can browse the database by topic or browse or search by keyword. A separate list of the full-text publications is also provided. A useful site for students and professionals in the tourism industry.

239

FishTraits Database  

USGS Publications Warehouse

The need for integrated and widely accessible sources of species traits data to facilitate studies of ecology, conservation, and management has motivated development of traits databases for various taxa. In spite of the increasing number of traits-based analyses of freshwater fishes in the United States, no consolidated database of traits of this group exists publicly, and much useful information on these species is documented only in obscure sources. The largely inaccessible and unconsolidated traits information makes large-scale analysis involving many fishes and/or traits particularly challenging. FishTraits is a database of >100 traits for 809 (731 native and 78 exotic) fish species found in freshwaters of the conterminous United States, including 37 native families and 145 native genera. The database contains information on four major categories of traits: (1) trophic ecology, (2) body size and reproductive ecology (life history), (3) habitat associations, and (4) salinity and temperature tolerances. Information on geographic distribution and conservation status is also included. Together, we refer to the traits, distribution, and conservation status information as attributes. Descriptions of attributes are available here. Many sources were consulted to compile attributes, including state and regional species accounts and other databases.

Angermeier, Paul L.; Frimpong, Emmanuel A.

2009-01-01

240

Single-nucleotide polymorphisms in genes relating to homocysteine metabolism: how applicable are public SNP databases to a typical European population?  

Microsoft Academic Search

To facilitate the association studies in complex diseases characterized by hyperhomocysteinemia, we collected structural and frequency data on single-nucleotide polymorphism (SNPs) in 24 genes relating to homocysteine metabolism. Firstly, we scanned ?1.2 Mbp of sequence in the NCBI SNP database (dbSNP) build 110 and we detected 1353 putative SNPs with an average in silico genic density of 1:683. Out of

Bohumila Janošíková; Petra Zavadáková; Viktor Kožich

2005-01-01

241

Scientists Report New Online Cancer Research Databases  

Cancer.gov

Like the old saying "art for art's sake," most medical researchers once believed that creating large computer databases of known genes or DNA sequences was a case of gathering information for the sake of gathering information.

242

MetaBase—the wiki-database of biological databases  

PubMed Central

Biology is generating more data than ever. As a result, there is an ever increasing number of publicly available databases that analyse, integrate and summarize the available data, providing an invaluable resource for the biological community. As this trend continues, there is a pressing need to organize, catalogue and rate these resources, so that the information they contain can be most effectively exploited. MetaBase (MB) (http://MetaDatabase.Org) is a community-curated database containing more than 2000 commonly used biological databases. Each entry is structured using templates and can carry various user comments and annotations. Entries can be searched, listed, browsed or queried. The database was created using the same MediaWiki technology that powers Wikipedia, allowing users to contribute on many different levels. The initial release of MB was derived from the content of the 2007 Nucleic Acids Research (NAR) Database Issue. Since then, approximately 100 databases have been manually collected from the literature, and users have added information for over 240 databases. MB is synchronized annually with the static Molecular Biology Database Collection provided by NAR. To date, there have been 19 significant contributors to the project; each one is listed as an author here to highlight the community aspect of the project. PMID:22139927

Bolser, Dan M.; Chibon, Pierre-Yves; Palopoli, Nicolas; Gong, Sungsam; Jacob, Daniel; Angel, Victoria Dominguez Del; Swan, Dan; Bassi, Sebastian; González, Virginia; Suravajhala, Prashanth; Hwang, Seungwoo; Romano, Paolo; Edwards, Rob; Bishop, Bryan; Eargle, John; Shtatland, Timur; Provart, Nicholas J.; Clements, Dave; Renfro, Daniel P.; Bhak, Daeui; Bhak, Jong

2012-01-01

243

The Porcelain Crab Transcriptome and PCAD, the Porcelain Crab Microarray and Sequence Database  

SciTech Connect

Background: With the emergence of a completed genome sequence of the freshwater crustacean Daphnia pulex, construction of genomic-scale sequence databases for additional crustacean sequences are important for comparative genomics and annotation. Porcelain crabs, genus Petrolisthes, have been powerful crustacean models for environmental and evolutionary physiology with respect to thermal adaptation and understanding responses of marine organisms to climate change. Here, we present a large-scale EST sequencing and cDNA microarray database project for the porcelain crab Petrolisthes cinctipes. Methodology/Principal Findings: A set of ~;;30K unique sequences (UniSeqs) representing ~;;19K clusters were generated from ~;;98K high quality ESTs from a set of tissue specific non-normalized and mixed-tissue normalized cDNA libraries from the porcelain crab Petrolisthes cinctipes. Homology for each UniSeq was assessed using BLAST, InterProScan, GO and KEGG database searches. Approximately 66percent of the UniSeqs had homology in at least one of the databases. All EST and UniSeq sequences along with annotation results and coordinated cDNA microarray datasets have been made publicly accessible at the Porcelain Crab Array Database (PCAD), a feature-enriched version of the Stanford and Longhorn Array Databases.Conclusions/Significance: The EST project presented here represents the third largest sequencing effort for any crustacean, and the largest effort for any crab species. Our assembly and clustering results suggest that our porcelain crab EST data set is equally diverse to the much larger EST set generated in the Daphnia pulex genome sequencing project, and thus will be an important resource to the Daphnia research community. Our homology results support the pancrustacea hypothesis and suggest that Malacostraca may be ancestral to Branchiopoda and Hexapoda. Our results also suggest that our cDNA microarrays cover as much of the transcriptome as can reasonably be captured in EST library sequencing approaches, and thus represent a rich resource for studies of environmental genomics.

Tagmount, Abderrahmane; Wang, Mei; Lindquist, Erika; Tanaka, Yoshihiro; Teranishi, Kristen S.; Sunagawa, Shinichi; Wong, Mike; Stillman, Jonathon H.

2010-01-27

244

The results of an mtDNA study of 1200 inhabitants of a German village in comparison to other Caucasian databases and its relevance for forensic casework  

Microsoft Academic Search

Mitochondrial DNA control region sequences were determined in 1200 male volunteers from one village area of Lower Saxony\\u000a for the hypervariable region 1 (HV1). The 154 variable positions found resulted in 460 different haplotypes with a haplotype\\u000a diversity value of 0.98165. The number of different haplotypes showed a nearly linear increase with the number of individuals\\u000a typed. The haplotype diversity

H. Pfeiffer; P. Forster; C. Ortmann; B. Brinkmann

2001-01-01

245

The Hawaiian Freshwater Algal Database (HfwADB): a laboratory LIMS and online biodiversity resource  

PubMed Central

Background Biodiversity databases serve the important role of highlighting species-level diversity from defined geographical regions. Databases that are specially designed to accommodate the types of data gathered during regional surveys are valuable in allowing full data access and display to researchers not directly involved with the project, while serving as a Laboratory Information Management System (LIMS). The Hawaiian Freshwater Algal Database, or HfwADB, was modified from the Hawaiian Algal Database to showcase non-marine algal specimens collected from the Hawaiian Archipelago by accommodating the additional level of organization required for samples including multiple species. Description The Hawaiian Freshwater Algal Database is a comprehensive and searchable database containing photographs and micrographs of samples and collection sites, geo-referenced collecting information, taxonomic data and standardized DNA sequence data. All data for individual samples are linked through unique 10-digit accession numbers (“Isolate Accession”), the first five of which correspond to the collection site (“Environmental Accession”). Users can search online for sample information by accession number, various levels of taxonomy, habitat or collection site. HfwADB is hosted at the University of Hawaii, and was made publicly accessible in October 2011. At the present time the database houses data for over 2,825 samples of non-marine algae from 1,786 collection sites from the Hawaiian Archipelago. These samples include cyanobacteria, red and green algae and diatoms, as well as lesser representation from some other algal lineages. Conclusions HfwADB is a digital repository that acts as a Laboratory Information Management System for Hawaiian non-marine algal data. Users can interact with the repository through the web to view relevant habitat data (including geo-referenced collection locations) and download images of collection sites, specimen photographs and micrographs, and DNA sequences. It is publicly available at http://algae.manoa.hawaii.edu/hfwadb/. PMID:23095476

2012-01-01

246

INVADERS Database  

NSDL National Science Digital Library

Based at the University of Montana and directed by Dr. Peter Rice, the INVADERS Database is "a comprehensive database of exotic plant names and weed distribution records for five states in the northwestern United States." Designed for use by land management and weed regulatory agencies, INVADERS uses a query interface (plant name or location) to sort and display information. Data are updated regularly so as to increase the chance of detecting and halting the rapid spread of alien weeds. Highlights of the site include the noxious weed listings for all US states and six Canadian provinces, historic distribution records against which to compare current plant distributions, and summary statistics such as the number of invasive species detected per state or a summary of the 120 year invasion, among others. The INVADERS database will prove both interesting and useful to managers and academics, alike.

247

Solubility Database  

National Institute of Standards and Technology Data Gateway

SRD 106 IUPAC-NIST Solubility Database (Web, free access)   These solubilities are compiled from 18 volumes (Click here for List) of the International Union for Pure and Applied Chemistry(IUPAC)-NIST Solubility Data Series. The database includes liquid-liquid, solid-liquid, and gas-liquid systems. Typical solvents and solutes include water, seawater, heavy water, inorganic compounds, and a variety of organic compounds such as hydrocarbons, halogenated hydrocarbons, alcohols, acids, esters and nitrogen compounds. There are over 67,500 solubility measurements and over 1800 references.

248

Databases and software for the analysis of mutations in the human p53 gene, human hprt gene and both the lacI and lacZ gene in transgenic rodents.  

PubMed

We have created databases and software applications for the analysis of DNA mutations at the human p53 gene, the human hprt gene and both the rodent transgenic lacI and lacZ loci. The databases themselves are stand-alone dBASE files and the software for analysis of the databases runs on IBM-compatible computers with Microsoft Windows. Each database has a separate software analysis program. The software created for these databases permit the filtering, ordering, report generation and display of information in the database. In addition, a significant number of routines have been developed for the analysis of single base substitutions. One method of obtaining the databases and software is via the World Wide Web. Open the following home page with a Web Browser: http://sunsite.unc.edu/dnam/mainpage. html . Alternatively, the databases and programs are available via public FTP from: anonymous@sunsite.unc.edu. There is no password required to enter the system. The databases and software are found beneath the subdirectory: pub/academic/biology/dna-mutations. Two other programs are available at the site, a program for comparison of mutational spectra and a program for entry of mutational data into a relational database. PMID:9399835

Cariello, N F; Douglas, G R; Gorelick, N J; Hart, D W; Wilson, J D; Soussi, T

1998-01-01

249

Databases and software for the analysis of mutations in the human p53 gene, the human hprt gene and both the lacI and lacZ gene in transgenic rodents.  

PubMed

We have created databases and software applications for the analysis of DNA mutations at the humanp53gene, the humanhprtgene and both the rodent transgeniclacIandlacZlocus. The databases themselves are stand-alone dBASE files and the software for analysis of the databases runs on IBM-compatible computers. Each database has a separate software analysis program. The software created for these databases permit the filtering, ordering, report generation and display of information in the database. In addition, a significant number of routines have been developed for the analysis of single base substitutions. One method of obtaining the databases and software is via the World Wide Web (WWW). Open the following home page with a Web Browser: http://sunsite.unc.edu/dnam/mainpage.ht ml . Alternatively, the databases and programs are available via public FTP from: anonymous@sunsite.unc.edu . There is no password required to enter the system. The databases and software are found beneath the subdirectory: pub/academic/biology/dna-mutations. Two other programs are available at the site-a program for comparison of mutational spectra and a program for entry of mutational data into a relational database. PMID:9016522

Cariello, N F; Douglas, G R; Dycaico, M J; Gorelick, N J; Provost, G S; Soussi, T

1997-01-01

250

Avibase: The World Bird Database  

NSDL National Science Digital Library

This database provides information on all birds of the world, featuring information on thousands of species and subspecies of birds such as taxonomy, names and synonyms in various languages, photos, distribution maps, and links to additional information from other websites. The database is searchable by keyword or term, exact name, language, year of publication, and other parameters. There is also a search by taxonomic family, a set of checklists by geographic region, and a blog for ornithological discussions.

Lepage, Denis

251

American Mineralogist Crystal Structure Database  

NSDL National Science Digital Library

This database provides access to information on every crystal structure published in the American Mineralogist, the Canadian Mineralogist, European Journal of Mineralogy, and Physics and Chemistry of Minerals, as well as selected datasets from other journals. The data are searchable by mineral name, author, chemistry, cell parameters and symmetry, diffraction pattern, and a general search. There are also lists of minerals represented in the database and authors of publications cited.

R. T. Downs

252

Database of recent tsunami deposits  

USGS Publications Warehouse

This report describes a database of sedimentary characteristics of tsunami deposits derived from published accounts of tsunami deposit investigations conducted shortly after the occurrence of a tsunami. The database contains 228 entries, each entry containing data from up to 71 categories. It includes data from 51 publications covering 15 tsunamis distributed between 16 countries. The database encompasses a wide range of depositional settings including tropical islands, beaches, coastal plains, river banks, agricultural fields, and urban environments. It includes data from both local tsunamis and teletsunamis. The data are valuable for interpreting prehistorical, historical, and modern tsunami deposits, and for the development of criteria to identify tsunami deposits in the geologic record.

Peters, Robert; Jaffe, Bruce E.

2010-01-01

253

Mineralogy Database  

NSDL National Science Digital Library

This is a large database of minerals that can be sorted either alphabetically or arranged systematically. Users can access minerals by name, elements, sulfides, halides, oxides, carbonates, sulfates, phosphates, silicates, organic minerals, or by variety. Once located, the properties of the mineral are displayed, including its chemical formula, crystal system, and location. Users can also access photos of minerals.

254

COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems.  

PubMed

The COXPRESdb (http://coxpresdb.jp) provides gene coexpression relationships for animal species. Here, we report the updates of the database, mainly focusing on the following two points. For the first point, we added RNAseq-based gene coexpression data for three species (human, mouse and fly), and largely increased the number of microarray experiments to nine species. The increase of the number of expression data with multiple platforms could enhance the reliability of coexpression data. For the second point, we refined the data assessment procedures, for each coexpressed gene list and for the total performance of a platform. The assessment of coexpressed gene list now uses more reasonable P-values derived from platform-specific null distribution. These developments greatly reduced pseudo-predictions for directly associated genes, thus expanding the reliability of coexpression data to design new experiments and to discuss experimental results. PMID:25392420

Okamura, Yasunobu; Aoki, Yuichi; Obayashi, Takeshi; Tadaka, Shu; Ito, Satoshi; Narise, Takafumi; Kinoshita, Kengo

2015-01-28

255

The 2013 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection  

PubMed Central

The 20th annual Database Issue of Nucleic Acids Research includes 176 articles, half of which describe new online molecular biology databases and the other half provide updates on the databases previously featured in NAR and other journals. This year’s highlights include two databases of DNA repeat elements; several databases of transcriptional factors and transcriptional factor-binding sites; databases on various aspects of protein structure and protein–protein interactions; databases for metagenomic and rRNA sequence analysis; and four databases specifically dedicated to Escherichia coli. The increased emphasis on using the genome data to improve human health is reflected in the development of the databases of genomic structural variation (NCBI’s dbVar and EBI’s DGVa), the NIH Genetic Testing Registry and several other databases centered on the genetic basis of human disease, potential drugs, their targets and the mechanisms of protein–ligand binding. Two new databases present genomic and RNAseq data for monkeys, providing wealth of data on our closest relatives for comparative genomics purposes. The NAR online Molecular Biology Database Collection, available at http://www.oxfordjournals.org/nar/database/a/, has been updated and currently lists 1512 online databases. The full content of the Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/). PMID:23203983

Fernández-Suárez, Xosé M.; Galperin, Michael Y.

2013-01-01

256

The AMMA database  

NASA Astrophysics Data System (ADS)

The AMMA project includes aircraft, ground-based and ocean measurements, an intensive use of satellite data and diverse modelling studies. Therefore, the AMMA database aims at storing a great amount and a large variety of data, and at providing the data as rapidly and safely as possible to the AMMA research community. In order to stimulate the exchange of information and collaboration between researchers from different disciplines or using different tools, the database provides a detailed description of the products and uses standardized formats. The AMMA database contains: - AMMA field campaigns datasets; - historical data in West Africa from 1850 (operational networks and previous scientific programs); - satellite products from past and future satellites, (re-)mapped on a regular latitude/longitude grid and stored in NetCDF format (CF Convention); - model outputs from atmosphere or ocean operational (re-)analysis and forecasts, and from research simulations. The outputs are processed as the satellite products are. Before accessing the data, any user has to sign the AMMA data and publication policy. This chart only covers the use of data in the framework of scientific objectives and categorically excludes the redistribution of data to third parties and the usage for commercial applications. Some collaboration between data producers and users, and the mention of the AMMA project in any publication is also required. The AMMA database and the associated on-line tools have been fully developed and are managed by two teams in France (IPSL Database Centre, Paris and OMP, Toulouse). Users can access data of both data centres using an unique web portal. This website is composed of different modules : - Registration: forms to register, read and sign the data use chart when an user visits for the first time - Data access interface: friendly tool allowing to build a data extraction request by selecting various criteria like location, time, parameters... The request can concern local, satellite and model data. - Documentation: catalogue of all the available data and their metadata. These tools have been developed using standard and free languages and softwares: - Linux system with an Apache web server and a Tomcat application server; - J2EE tools : JSF and Struts frameworks, hibernate; - relational database management systems: PostgreSQL and MySQL; - OpenLDAP directory. In order to facilitate the access to the data by African scientists, the complete system has been mirrored at AGHRYMET Regional Centre in Niamey and is operational there since January 2009. Users can now access metadata and request data through one or the other of two equivalent portals: http://database.amma-international.org or http://amma.agrhymet.ne/amma-data.

Boichard, Jean-Luc; Brissebrat, Guillaume; Cloche, Sophie; Eymard, Laurence; Fleury, Laurence; Mastrorillo, Laurence; Moulaye, Oumarou; Ramage, Karim

2010-05-01

257

XMAn: a Homo sapiens mutated-peptide database for the MS analysis of cancerous cell states.  

PubMed

To enable the identification of mutated peptide sequences in complex biological samples, in this work, two novel cancer- and disease-related protein databases with mutation information collected from several public resources such as COSMIC, IARC P53, OMIM, and UniProtKB were developed. In-house developed Perl scripts were used to search and process the data and to translate each gene-level mutation into a mutated peptide sequence. The cancer and disease mutation databases comprise a total of 872,125 and 27,148 peptide entries from 25?642 and 2913 proteins, respectively. A description line for each entry provides the parent protein ID and name, the cDNA- and protein-level mutation site and type, the originating database, and the disease or cancer tissue type and corresponding hits. The two databases are FASTA-formatted to enable data retrieval by commonly used tandem MS search engines. While the largest number of mutations were encountered for the amino acids A/D/E/G/L/P/R/S, the global mutation profiles replicate closely the outcome of the 1000 Genomes Project aimed at cataloguing natural mutations in the human population. The affected proteins were primarily involved in transcription regulation, splicing, protein synthesis/folding/binding, redox/energy production, adhesion/motility, and to some extent in DNA damage repair and signaling. The applicability of the database to identifying the presence of mutated peptides was investigated with MCF-7 breast cancer cell extracts. PMID:25211293

Yang, Xu; Lazar, Iulia M

2014-12-01

258

FishMicrosat: a microsatellite database of commercially important fishes and shellfishes of the Indian subcontinent  

PubMed Central

Background Microsatellite DNA is one of many powerful genetic markers used for the construction of genetic linkage maps and the study of population genetics. The biological databases in public domain hold vast numbers of microsatellite sequences for many organisms including fishes. The microsatellite data available in these data sources were extracted and managed into a database that facilitates sequences analysis and browsing relevant information. The system also helps to design primer sequences for flanking regions of repeat loci for PCR identification of polymorphism within populations. Description FishMicrosat is a database of microsatellite sequences of fishes and shellfishes that includes important aquaculture species such as Lates calcarifer, Ctenopharyngodon idella, Hypophthalmichthys molitrix, Penaeus monodon, Labeo rohita, Oreochromis niloticus, Fenneropenaeus indicus and Macrobrachium rosenbergii. The database contains 4398 microsatellite sequences of 41 species belonging to 15 families from the Indian subcontinent. GenBank of NCBI was used as a prime data source for developing the database. The database presents information about simple and compound microsatellites, their clusters and locus orientation within sequences. The database has been integrated with different tools in a web interface such as primer designing, locus finding, mapping repeats, detecting similarities among sequences across species, and searching using motifs and keywords. In addition, the database has the ability to browse information on the top 10 families and the top 10 species, through record overview. Conclusions FishMicrosat database is a useful resource for fish and shellfish microsatellite analyses and locus identification across species, which has important applications in population genetics, evolutionary studies and genetic relatedness among species. The database can be expanded further to include the microsatellite data of fishes and shellfishes from other regions and available information on genome sequencing project of species of aquaculture importance. PMID:24047532

2013-01-01

259

TreeGenes: A Forest Tree Genome Database  

PubMed Central

The Dendrome Project and associated TreeGenes database serve the forest genetics research community through a curated and integrated web-based relational database. The research community is composed of approximately 2 000 members representing over 730 organizations worldwide. The database itself is composed of a wide range of genetic data from many forest trees with focused efforts on commercially important members of the Pinaceae family. The primary data types curated include species, publications, tree and DNA extraction information, genetic maps, molecular markers, ESTs, genotypic, and phenotypic data. There are currently ten main search modules or user access points within this PostgreSQL database. These access points allow users to navigate logically through the related data types. The goals of the Dendrome Project are to (1) provide a comprehensive resource for forest tree genomics data to facilitate gene discovery in related species, (2) develop interfaces that encourage the submission and integration of all genomic data, and to (3) centralize and distribute existing and novel online tools for the research community that both support and ease analysis. Recent developments have focused on increasing data content, functional annotations, data retrieval, and visualization tools. TreeGenes was developed to provide a centralized web resource with analysis and visualization tools to support data storage and exchange. PMID:18725987

Wegrzyn, Jill L.; Lee, Jennifer M.; Tearse, Brandon R.; Neale, David B.

2008-01-01

260

Introduction to Database Database Systems Lecture 1  

E-print Network

Introduction to Database Systems Database Systems Lecture 1 Natasha Alechina www.cs.nott.ac.uk/~nza/G51DBS #12;In this Lecture · Course Information · Databases and Database Systems · Some History questions · Format similar to previous years. #12;Textbook · Recommended textbooks: · `Database Systems

Alechina, Natasha

261

Molecular Identification and Databases in Fusarium  

Technology Transfer Automated Retrieval System (TEKTRAN)

DNA sequence-based methods for identifying pathogenic and mycotoxigenic Fusarium isolates have become the gold standard worldwide. Moreover, fusarial DNA sequence data are increasing rapidly in several web-accessible databases for comparative purposes. Unfortunately, the use of Basic Alignment Sea...

262

Databases for T-cell epitopes.  

PubMed

Modem immunology and vaccinology incorporate immunoinformatics techniques to give insights into immune systems and accelerate vaccine design. Databases managing epitope data in a structured form with immune-related annotations including sequences, alleles, source organisms, structures, and diseases could be the most crucial part of immunoinformatics offering data sources for the analysis of immune systems and development of prediction methods. This chapter provides an overview of publicly available databases of T-cell epitopes including general databases, pathogen- and tumor-specific databases, and 3D structure databases. PMID:25048121

Tung, Chun-Wei

2014-01-01

263

TRedD--a database for tandem repeats over the edit distance.  

PubMed

A 'tandem repeat' in DNA is a sequence of two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats are common in the genomes of both eukaryotic and prokaryotic organisms. They are significant markers for human identity testing, disease diagnosis, sequence homology and population studies. In this article, we describe a new database, TRedD, which contains the tandem repeats found in the human genome. The database is publicly available online, and the software for locating the repeats is also freely available. The definition of tandem repeats used by TRedD is a new and innovative definition based upon the concept of 'evolutive tandem repeats'. In addition, we have developed a tool, called TandemGraph, to graphically depict the repeats occurring in a sequence. This tool can be coupled with any repeat finding software, and it should greatly facilitate analysis of results. Database URL: http://tandem.sci.brooklyn.cuny.edu/ PMID:20624712

Sokol, Dina; Atagun, Firat

2010-01-01

264

Physiological Parameters Database for PBPK Modeling (External Review Draft)  

EPA Science Inventory

EPA released for public comment a physiological parameters database (created using Microsoft ACCESS) intended to be used in PBPK modeling. The database contains physiological parameter values for humans from early childhood through senescence. It also contains similar data for an...

265

A Chronostratigraphic Relational Database Ontology  

NASA Astrophysics Data System (ADS)

A chronostratigraphic research database was donated by British Petroleum to the Stratigraphy Group at the Energy and Geoscience Institute (EGI), University of Utah. These data consists of over 2,000 measured sections representing over three decades of research into the application of the graphic correlation method. The data are global and includes both microfossil (foraminifera, calcareous nannoplankton, spores, pollen, dinoflagellate cysts, etc) and macrofossil data. The objective of the donation was to make the research data available to the public in order to encourage additional chronostratigraphy studies, specifically regarding graphic correlation. As part of the National Science Foundation's Cyberinfrastructure for the Geosciences (GEON) initiative these data have been made available to the public at http://css.egi.utah.edu. To encourage further research using the graphic correlation method, EGI has developed a software package, StrataPlot that will soon be publicly available from the GEON website as a standalone software download. The EGI chronostratigraphy research database, although relatively large, has many data holes relative to some paleontological disciplines and geographical areas, so the challenge becomes how do we expand the data available for chronostratigrahic studies using graphic correlation. There are several public or soon-to-be public databases available to chronostratigraphic research, but they have their own data structures and modes of presentation. The heterogeneous nature of these database schemas hinders their integration and makes it difficult for the user to retrieve and consolidate potentially valuable chronostratigraphic data. The integration of these data sources would facilitate rapid and comprehensive data searches, thus helping advance studies in chronostratigraphy. The GEON project will host a number of databases within the geology domain, some of which contain biostratigraphic data. Ontologies are being developed to provide an integrated query system for the searching across GEON's biostratigraphy databases, as well as databases available in the public domain. Although creating an ontology directly from the existing database metadata would have been effective and straightforward, our effort was directed towards creating a more efficient representation of our database, as well as a general representation of the biostratigraphic domain.

Platon, E.; Gary, A.; Sikora, P.

2005-12-01

266

CBS Databases  

NSDL National Science Digital Library

This major reference center for mycologists traces its existence back to 1903. Now an institute of the Royal Netherlands Academy of Arts and Sciences, CBS (Centraalbureau voor Schimmelcultures) continues to maintain and distribute one of the largest collections of living fungi in the world. With over 35,000 strains, "the collection contains representatives of virtually all fungal groups that can be cultured." Users can currently search six databases containing over 72,000 strains of fungi, yeasts, and bacteria held at CBS or other institutions. Each database offers several search options, such as by Species Name, Strain Number, or Properties of species/ strains. Search returns include Species, Variety, relevant Literature, Strain Number, Origin, History, and Form of Supply. The site also offers articles in HTML and .pdf format, information on current research themes and projects, strain ordering information, and an image gallery.

267

Trail Database  

NSDL National Science Digital Library

Something of a veteran by Internet standards, the Trail Database has been around since 1997 and, as such, now bills itself as the "world's largest hiking trail database." "Henk," the Dutch hiker responsible for this compendium, updates the site regularly and has included a wide variety of links to helpful material here. Users can search or browse the resources, which are arranged both under general topics, such as Knots or Equipment, and by country. Those planning European hikes will find the links off the front page to foot and mouth disease-related hiking restrictions useful (though we found some of these links to be broken). In all, an impressive collection of material. The site is available in Dutch or English.

1997-01-01

268

ARTI Refrigerant Database  

SciTech Connect

The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air- conditioning and refrigeration equipment. The database identifies sources of specific information on R-32, R-123, R-124, R-125, R-134, R-134a, R-141b, R-142b, R-143a, R-152a, R-245ca, R-290 (propane), R- 717 (ammonia), ethers, and others as well as azeotropic and zeotropic and zeotropic blends of these fluids. It addresses lubricants including alkylbenzene, polyalkylene glycol, ester, and other synthetics as well as mineral oils. It also references documents on compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. A computerized version is available that includes retrieval software.

Calm, J.M.

1992-11-09

269

Protein Model Database  

SciTech Connect

The phenomenal success of the genome sequencing projects reveals the power of completeness in revolutionizing biological science. Currently it is possible to sequence entire organisms at a time, allowing for a systemic rather than fractional view of their organization and the various genome-encoded functions. There is an international plan to move towards a similar goal in the area of protein structure. This will not be achieved by experiment alone, but rather by a combination of efforts in crystallography, NMR spectroscopy, and computational modeling. Only a small fraction of structures are expected to be identified experimentally, the remainder to be modeled. Presently there is no organized infrastructure to critically evaluate and present these data to the biological community. The goal of the Protein Model Database project is to create such infrastructure, including (1) public database of theoretically derived protein structures; (2) reliable annotation of protein model quality, (3) novel structure analysis tools, and (4) access to the highest quality modeling techniques available.

Fidelis, K; Adzhubej, A; Kryshtafovych, A; Daniluk, P

2005-02-23

270

The IPD and IMGT/HLA database: allele variant databases.  

PubMed

The Immuno Polymorphism Database (IPD) was developed to provide a centralized system for the study of polymorphism in genes of the immune system. Through the IPD project we have established a central platform for the curation and publication of locus-specific databases involved either directly or related to the function of the Major Histocompatibility Complex in a number of different species. We have collaborated with specialist groups or nomenclature committees that curate the individual sections before they are submitted to IPD for online publication. IPD consists of five core databases, with the IMGT/HLA Database as the primary database. Through the work of the various nomenclature committees, the HLA Informatics Group and in collaboration with the European Bioinformatics Institute we are able to provide public access to this data through the website http://www.ebi.ac.uk/ipd/. The IPD project continues to develop with new tools being added to address scientific developments, such as Next Generation Sequencing, and to address user feedback and requests. Regular updates to the website ensure that new and confirmatory sequences are dispersed to the immunogenetics community, and the wider research and clinical communities. PMID:25414341

Robinson, James; Halliwell, Jason A; Hayhurst, James D; Flicek, Paul; Parham, Peter; Marsh, Steven G E

2015-01-28

271

A Novel Approach: Chemical Relational Databases, and the Role of the ISSCAN Database on Assessing Chemical Carcinogenity  

EPA Science Inventory

Mutagenicity and carcinogenicity databases are crucial resources for toxicologists and regulators involved in chemicals risk assessment. Until recently, existing public toxicity databases have been constructed primarily as "look-up-tables" of existing data, and most often did no...

272

45 CFR 1356.80 - Scope of the National Youth in Transition Database.  

Code of Federal Regulations, 2010 CFR

...Scope of the National Youth in Transition Database. 1356.80 Section 1356.80 Public...Scope of the National Youth in Transition Database. The requirements of the National Youth in Transition Database (NYTD) §§ 1356.81 through...

2010-10-01

273

45 CFR 1356.80 - Scope of the National Youth in Transition Database.  

Code of Federal Regulations, 2011 CFR

...Scope of the National Youth in Transition Database. 1356.80 Section 1356.80 Public...Scope of the National Youth in Transition Database. The requirements of the National Youth in Transition Database (NYTD) §§ 1356.81 through...

2011-10-01

274

45 CFR 1356.80 - Scope of the National Youth in Transition Database.  

Code of Federal Regulations, 2014 CFR

...Scope of the National Youth in Transition Database. 1356.80 Section 1356.80 Public...Scope of the National Youth in Transition Database. The requirements of the National Youth in Transition Database (NYTD) §§ 1356.81 through...

2014-10-01

275

45 CFR 1356.80 - Scope of the National Youth in Transition Database.  

Code of Federal Regulations, 2013 CFR

...Scope of the National Youth in Transition Database. 1356.80 Section 1356.80 Public...Scope of the National Youth in Transition Database. The requirements of the National Youth in Transition Database (NYTD) §§ 1356.81 through...

2013-10-01

276

45 CFR 1356.80 - Scope of the National Youth in Transition Database.  

Code of Federal Regulations, 2012 CFR

...Scope of the National Youth in Transition Database. 1356.80 Section 1356.80 Public...Scope of the National Youth in Transition Database. The requirements of the National Youth in Transition Database (NYTD) §§ 1356.81 through...

2012-10-01

277

Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants  

PubMed Central

In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops. PMID:25320561

Shirasawa, Kenta; Isobe, Sachiko; Tabata, Satoshi; Hirakawa, Hideki

2014-01-01

278

Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants.  

PubMed

In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops. PMID:25320561

Shirasawa, Kenta; Isobe, Sachiko; Tabata, Satoshi; Hirakawa, Hideki

2014-09-01

279

Open Geoscience Database  

NASA Astrophysics Data System (ADS)

Currently there is an enormous amount of various geoscience databases. Unfortunately the only users of the majority of the databases are their elaborators. There are several reasons for that: incompaitability, specificity of tasks and objects and so on. However the main obstacles for wide usage of geoscience databases are complexity for elaborators and complication for users. The complexity of architecture leads to high costs that block the public access. The complication prevents users from understanding when and how to use the database. Only databases, associated with GoogleMaps don't have these drawbacks, but they could be hardly named "geoscience" Nevertheless, open and simple geoscience database is necessary at least for educational purposes (see our abstract for ESSI20/EOS12). We developed a database and web interface to work with them and now it is accessible at maps.sch192.ru. In this database a result is a value of a parameter (no matter which) in a station with a certain position, associated with metadata: the date when the result was obtained; the type of a station (lake, soil etc); the contributor that sent the result. Each contributor has its own profile, that allows to estimate the reliability of the data. The results can be represented on GoogleMaps space image as a point in a certain position, coloured according to the value of the parameter. There are default colour scales and each registered user can create the own scale. The results can be also extracted in *.csv file. For both types of representation one could select the data by date, object type, parameter type, area and contributor. The data are uploaded in *.csv format: Name of the station; Lattitude(dd.dddddd); Longitude(ddd.dddddd); Station type; Parameter type; Parameter value; Date(yyyy-mm-dd). The contributor is recognised while entering. This is the minimal set of features that is required to connect a value of a parameter with a position and see the results. All the complicated data treatment could be conducted in other programs after extraction the filtered data into *.csv file. It makes the database understandable for non-experts. The database employs open data format (*.csv) and wide spread tools: PHP as the program language, MySQL as database management system, JavaScript for interaction with GoogleMaps and JQueryUI for create user interface. The database is multilingual: there are association tables, which connect with elements of the database. In total the development required about 150 hours. The database still has several problems. The main problem is the reliability of the data. Actually it needs an expert system for estimation the reliability, but the elaboration of such a system would take more resources than the database itself. The second problem is the problem of stream selection - how to select the stations that are connected with each other (for example, belong to one water stream) and indicate their sequence. Currently the interface is English and Russian. However it can be easily translated to your language. But some problems we decided. For example problem "the problem of the same station" (sometimes the distance between stations is smaller, than the error of position): when you adding new station to the database our application automatically find station near this place. Also we decided problem of object and parameter type (how to regard "EC" and "electrical conductivity" as the same parameter). This problem has been solved using "associative tables". If you would like to see the interface on your language, just contact us. We should send you the list of terms and phrases for translation on your language. The main advantage of the database is that it is totally open: everybody can see, extract the data from the database and use them for non-commercial purposes with no charge. Registered users can contribute to the database without getting paid. We hope, that it will be widely used first of all for education purposes, but professional scientists could use it also.

Bashev, A.

2012-04-01

280

An evaluation for cross-species proteomics research by publicly available expressed sequence tag database search using tandem mass spectral data.  

PubMed

With 1383 tandem mass spectra derived from 120 individual protein spots separated by the two-dimensional (2-D) gel electrophoresis of protein samples from three different species, comparative analyses were performed by searching the Expressed Sequence Tag (EST) database (DB) and the NCBI non-redundant (nr) DB of green plants, respectively, which uses the Mascot search engine to establish a statistical basis. It was confirmed that the former could identify more peptides manually validated by de novo sequencing (DNS) from fewer species in more closely phylogenetic relationships than the latter in a statistically significant manner. Our data demonstrated that correct peptide identifications were given low Mascot scores (e.g. 6-14) and incorrect peptide identifications were given high Mascot scores (e.g. 68-83). Our data also showed that the current evaluation approaches to protein assignments are unsatisfactory because a few 'false-positive' proteins are recognized and several 'false-negative' proteins are rescued by manual validation. PMID:16941525

Huang, Mei; Chen, Tong; Chan, ZhuLong

2006-01-01

281

Lighthouse Explorer Database  

NSDL National Science Digital Library

Spotted by ResearchBuzz, this site from the Lighthouse Depot, a "virtual community" (and store) for lighthouse enthusiasts, contains a database with information on over 1,300 lighthouses around the world. Visitors may browse the listings alphabetically, by category, by state or country, or search by keyword. Entries include name, location, supervising organization, contact information, email and Website when available, and in some cases a photo. Other useful information is also provided when available, such as the dates the lighthouse was built and operational, whether or not it is open to the public, and driving directions.

282

The Stanford Tissue Microarray Database  

Microsoft Academic Search

The Stanford Tissue Microarray Database (TMAD; http:\\/\\/tma.stanford.edu) is a public resource for disseminating annotated tissue images and associated expression data. Stanford University pathologists, researchers and their collaborators worldwide use TMAD for designing, viewing, scoring and analyzing their tissue microarrays. The use of tissue microarrays allows hundreds of human tissue cores to be simultaneously probed by antibodies to detect protein abundance

Robert J. Marinelli; Kelli Montgomery; Chih Long Liu; Nigam H. Shah; Wijan Prapong; Michael Nitzberg; Zachariah K. Zachariah; Gavin Sherlock; Yasodha Natkunam; Robert B. West; Matt Van De Rijn; Patrick O. Brown; Catherine A. Ball

2008-01-01

283

REFEREE: BIBLIOGRAPHIC DATABASE MANAGER, DOCUMENTATION  

EPA Science Inventory

The publication is the user's manual for 3.xx releases of REFEREE, a general-purpose bibliographic database management program for IBM-compatible microcomputers. The REFEREE software also is available from NTIS. The manual has two main sections--Quick Tour and References Guide--a...

284

USDA Forest Service Southern Research Station: Publications  

NSDL National Science Digital Library

This database contains publications in support of this group\\'s mission to create the science and technology needed to sustain and enhance southern forest ecosystems and the benefits they provide. The database can be searched by author, title, keyword, date range, and publication origin; publication number; and by the most recent publications added to the database. There are also online versions of Compass, a publication catalog of research products from scientists at SRS.

285

DNA BARCODING IN LAND PLANTS: DEVELOPING STANDARDS TO QUANTIFY AND MAXIMIZE SUCCESS.  

PubMed

The selection of a DNA barcode in plants has been impeded in part due to the relatively low rates of nucleotide substitution observed at the most accessible plastid markers. However, the absence of consensus also reflects a lack of standards for comparing potential barcode markers. While many publications have suggested a host of plant DNA barcodes, the studies cannot be readily compared with each other through any quantitative or statistical parameter, partly because they put forward no single compelling rationale relevant to the adoption of a DNA barcode in plants. Here, we argue that the efficacy of any particular plant DNA barcode selection should reflect the anticipated performance of the resulting barcode database in assignment of a query sequence to species. While legitimate scientific disagreement exists over the criteria relevant to "database performance", the notion gives a unifying rationale for prioritizing selection criteria. Accordingly, we suggest a measure of barcode efficacy based on the rationale of database performance, "the probability of correct identification" (PCI). Moreover, the definition of PCI is left flexible enough to handle most of the scientific disagreement over how to best evaluate DNA barcodes. Finally, we consider how different types of barcodes might require different methods of analysis and database design and indicate how the analysis might affect the selection of the most broadly effective barcode for land plants. PMID:19779570

Erickson, David L; Spouge, John; Resch, Alissa; Weigt, Lee A; Kress, W John

2008-11-01

286

The EMBL Nucleotide Sequence Database.  

PubMed

The EMBL Nucleotide Sequence Database (aka EMBL-Bank; http://www.ebi.ac.uk/embl/) incorporates, organises and distributes nucleotide sequences from all available public sources. EMBL-Bank is located and maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK. In an international collaboration with DDBJ (Japan) and GenBank (USA), data are exchanged amongst the collaborating databases on a daily basis. Major contributors to the EMBL database are individual scientists and genome project groups. Webin is the preferred web-based submission system for individual submitters, whilst automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via FTP, email and World Wide Web interfaces. EBI's Sequence Retrieval System (SRS), a network browser for databanks in molecular biology, integrates and links the main nucleotide and protein databases plus many other specialized databases. For sequence similarity searching, a variety of tools (e.g. Blitz, Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT. All resources can be accessed via the EBI home page at http://www.ebi.ac.uk. PMID:11752244

Stoesser, Guenter; Baker, Wendy; van den Broek, Alexandra; Camon, Evelyn; Garcia-Pastor, Maria; Kanz, Carola; Kulikova, Tamara; Leinonen, Rasko; Lin, Quan; Lombard, Vincent; Lopez, Rodrigo; Redaschi, Nicole; Stoehr, Peter; Tuli, Mary Ann; Tzouvara, Katerina; Vaughan, Robert

2002-01-01

287

Higher Education Providers HEIDI -Online Information Database  

E-print Network

Higher Education Providers HEIDI - Online Information Database HEIDI Equality Representative Bodies Education Providers Media Industry & Commerce Researchers Public RecordReviews Sector Bodies Equality Challenge Unit Quality Assurance Agency Universities & Colleges Employers Association Higher Education

Glasgow, University of

288

Using Online Databases in Corporate Issues Management.  

ERIC Educational Resources Information Center

Finds that corporate public relations practitioners felt they were able, using online database and information services, to intercept issues earlier in the "issue cycle" and thus enable their organizations to develop more "proactionary" or "catalytic" issues management repose strategies. (SR)

Thomsen, Steven R.

1995-01-01

289

Correlates of Access to Business Research Databases  

ERIC Educational Resources Information Center

This study examines potential correlates of business research database access through academic libraries serving top business programs in the United States. Results indicate that greater access to research databases is related to enrollment in graduate business programs, but not to overall enrollment or status as a public or private institution.…

Gottfried, John C.

2010-01-01

290

Development of steam generator vessel database  

Microsoft Academic Search

The purpose of this project was to collect publicly-available information on Steam Generator (SG) vessel integrity, abstract and summarize the information, and develop a database that could be used for identification of trends. The database developed includes information on 256 SGs (27 of them replacements for originally-installed SGs) in 75 operating Pressurized Water Reactor plants in the United States. The

R. K. Mattu; J. Lauderdale

1992-01-01

291

Semantic Dictionary Design for Database Interoperability  

Microsoft Academic Search

Criteria and techniques to support the establishment of a semantic dictionary for database interoperability are described. The techniques allow the analysis of conceptual schemas of databases in a federation and the definition and maintenance of concept hierarchies. Similarity-based criteria are used to evaluate concept closeness and, consequently, to generate concept hierarchies. Experimentation of the techniques in the public administration domain

Silvana Castano; Valeria De Antonellis

1997-01-01

292

NICMOS HISTORY DATABASE AND April 10, 1998  

E-print Network

1 NICMOS HISTORY DATABASE AND WEB TOOLS C. Tullos April 10, 1998 ABSTRACT The history of NICMOS on the World Wide Web. The history tool which allows queries on the data, is available to the public. 1. The Database and Data A convenient way of keeping a history of some of the NICMOS instrument parameters

Sirianni, Marco

293

The taming of an impossible child: a standardized all-in approach to the phylogeny of Hymenoptera using public database sequences  

PubMed Central

Background Enormous molecular sequence data have been accumulated over the past several years and are still exponentially growing with the use of faster and cheaper sequencing techniques. There is high and widespread interest in using these data for phylogenetic analyses. However, the amount of data that one can retrieve from public sequence repositories is virtually impossible to tame without dedicated software that automates processes. Here we present a novel bioinformatics pipeline for downloading, formatting, filtering and analyzing public sequence data deposited in GenBank. It combines some well-established programs with numerous newly developed software tools (available at http://software.zfmk.de/). Results We used the bioinformatics pipeline to investigate the phylogeny of the megadiverse insect order Hymenoptera (sawflies, bees, wasps and ants) by retrieving and processing more than 120,000 sequences and by selecting subsets under the criteria of compositional homogeneity and defined levels of density and overlap. Tree reconstruction was done with a partitioned maximum likelihood analysis from a supermatrix with more than 80,000 sites and more than 1,100 species. In the inferred tree, consistent with previous studies, "Symphyta" is paraphyletic. Within Apocrita, our analysis suggests a topology of Stephanoidea + (Ichneumonoidea + (Proctotrupomorpha + (Evanioidea + Aculeata))). Despite the huge amount of data, we identified several persistent problems in the Hymenoptera tree. Data coverage is still extremely low, and additional data have to be collected to reliably infer the phylogeny of Hymenoptera. Conclusions While we applied our bioinformatics pipeline to Hymenoptera, we designed the approach to be as general as possible. With this pipeline, it is possible to produce phylogenetic trees for any taxonomic group and to monitor new data and tree robustness in a taxon of interest. It therefore has great potential to meet the challenges of the phylogenomic era and to deepen our understanding of the tree of life. PMID:21851592

2011-01-01

294

ARTI refrigerant database  

SciTech Connect

The Refrigerant Database is an information system on alternative refrigerants, associated lubricants, and their use in air conditioning and refrigeration. It consolidates and facilitates access to property, compatibility, environmental, safety, application and other information. It provides corresponding information on older refrigerants, to assist manufacturers and those using alternative refrigerants, to make comparisons and determine differences. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air-conditioning and refrigeration equipment. The complete documents are not included, though some may be added at a later date. The database identifies sources of specific information on refrigerants. It addresses lubricants including alkylbenzene, polyalkylene glycol, polyolester, and other synthetics as well as mineral oils. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. Incomplete citations or abstracts are provided for some documents. They are included to accelerate availability of the information and will be completed or replaced in future updates. Citations in this report are divided into the following topics: thermophysical properties; materials compatibility; lubricants and tribology; application data; safety; test and analysis methods; impacts; regulatory actions; substitute refrigerants; identification; absorption and adsorption; research programs; and miscellaneous documents. Information is also presented on ordering instructions for the computerized version.

Calm, J.M. [Calm (James M.), Great Falls, VA (United States)] [Calm (James M.), Great Falls, VA (United States)

1996-04-15

295

ARTI refrigerant database  

SciTech Connect

The Refrigerant Database is an information system on alternative refrigerants, associated lubricants, and their use in air conditioning and refrigeration. It consolidates and facilitates access to property, compatibility, environmental, safety, application and other information. It provides corresponding information on older refrigerants, to assist manufactures and those using alternative refrigerants, to make comparisons and determine differences. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air-conditioning and refrigeration equipment. The complete documents are not included, though some may be added at a later date. The database identifies sources of specific information on many refrigerants including propane, ammonia, water, carbon dioxide, propylene, ethers, and others as well as azeotropic and zeotropic blends of these fluids. It addresses lubricants including alkylbenzene, polyalkylene glycol, polyolester, and other synthetics as well as mineral oils. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. Incomplete citations or abstracts are provided for some documents. They are included to accelerate availability of the information and will be completed or replaced in future updates.

Calm, J.M. [Calm (James M.), Great Falls, VA (United States)

1998-08-01

296

ARTI refrigerant database  

SciTech Connect

The Refrigerant Database is an information system on alternative refrigerants, associated lubricants, and their use in air conditioning and refrigeration. It consolidates and facilitates access to property, compatibility, environmental, safety, application and other information. It provides corresponding information on older refrigerants, to assist manufacturers and those using alterative refrigerants, to make comparisons and determine differences. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air-conditioning and refrigeration equipment. The complete documents are not included, though some may be added at a later date. The database identifies sources of specific information on various refrigerants. It addresses lubricants including alkylbenzene, polyalkylene glycol, polyolester, and other synthetics as well as mineral oils. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. Incomplete citations or abstracts are provided for some documents. They are included to accelerate availability of the information and will be completed or replaced in future updates.

Calm, J.M.

1997-02-01

297

ARTI Refrigerant Database  

SciTech Connect

The Refrigerant Database consolidates and facilitates access to information to assist industry in developing equipment using alternative refrigerants. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air-conditioning and refrigeration equipment. The complete documents are not included. The database identifies sources of specific information on R-32, R-123, R-124, R-125, R-134, R-134a, R-141b, R-142b, R-143a, R-152a, R-245ca, R-290 (propane), R-717 (ammonia), ethers, and others as well as azeotropic and zeotropic blends of these fluids. It addresses lubricants including alkylbenzene, polyalkylene glycol, ester, and other synthetics as well as mineral oils. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. Incomplete citations or abstracts are provided for some documents to accelerate availability of the information and will be completed or replaced in future updates.

Cain, J.M. (Calm (James M.), Great Falls, VA (United States))

1993-04-30

298

DNA Binding Properties of TAF1 Isoforms with Two AT-hooks* Received for publication,June 30, 2006 Published, JBC Papers in Press,August 7, 2006, DOI 10.1074/jbc.M606289200  

E-print Network

DNA Binding Properties of TAF1 Isoforms with Two AT-hooks* Received for publication,June 30, 2006 AT-hook motifs, one of which is encoded by an alternatively spliced exon. Electrophoretic mobility for the sequence AAT. Alanine-scanning mutagenesis of the alterna- tively spliced AT-hook indicated that Lys

Wassarman, David A.

299

Increased coverage of protein families with the Blocks Database servers  

Microsoft Academic Search

The Blocks Database WWW (http:\\/\\/blocks.fhcrc.org ) and Email (blocks@blocks.fhcrc.org ) servers provide tools to search DNA and protein queries against the Blocks+ Database of multiple alignments, which represent conserved protein regions. Blocks+ nearly doubles the number of protein families included in the database by adding families from the Pfam-A, ProDom and Domo databases to those from PROSITE and PRINTS. Other

Jorja G. Henikoff; Elizabeth A. Greene; Shmuel Pietrokovski; Steven Henikoff

2000-01-01

300

RiboaptDB: A Comprehensive Database of Ribozymes and Aptamers  

PubMed Central

Background Catalytic RNA molecules are called ribozymes. The aptamers are DNA or RNA molecules that have been selected from vast populations of random sequences, through a combinatorial approach known as SELEX. The selected oligo-nucleotide sequences (~200 bp in length) have the ability to recognize a broad range of specific ligands by forming binding pockets. These novel aptamer sequences can bind to nucleic acids, proteins or small organic and inorganic chemical compounds and have many potential uses in medicine and technology. Results The comprehensive sequence information on aptamers and ribozymes that have been generated by in vitro selection methods are included in this RiboaptDB database. Such types of unnatural data generated by in vitro methods are not available in the public 'natural' sequence databases such as GenBank and EMBL. The amount of sequence data generated by in vitro selection experiments has been accumulating exponentially. There are 370 artificial ribozyme sequences and 3842 aptamer sequences in the total 4212 sequences from 423 citations in this RiboaptDB. We included general search feature, and individual feature wise search, user submission form for new data through online and also local BLAST search. Conclusion This database, besides serving as a storehouse of sequences that may have diagnostic or therapeutic utility in medicine, provides valuable information for computational and theoretical biologists. The RiboaptDB is extremely useful for garnering information about in vitro selection experiments as a whole and for better understanding the distribution of functional nucleic acids in sequence space. The database is updated regularly and is publicly available at . PMID:17118149

Thodima, Venkata; Pirooznia, Mehdi; Deng, Youping

2006-01-01

301

Mouse Phenome Database (MPD).  

PubMed

The Mouse Phenome Project was launched a decade ago to complement mouse genome sequencing efforts by promoting new phenotyping initiatives under standardized conditions and collecting the data in a central public database, the Mouse Phenome Database (MPD; http://phenome.jax.org). MPD houses a wealth of strain characteristics data to facilitate the use of the laboratory mouse in translational research for human health and disease, helping alleviate problems involving experimentation in humans that cannot be done practically or ethically. Data sets are voluntarily contributed by researchers from a variety of institutions and settings, or in some cases, retrieved by MPD staff from public sources. MPD maintains a growing collection of standardized reference data that assists investigators in selecting mouse strains for research applications; houses treatment/control data for drug studies and other interventions; offers a standardized platform for discovering genotype-phenotype relationships; and provides tools for hypothesis testing. MPD improvements and updates since our last NAR report are presented, including the addition of new tools and features to facilitate navigation and data mining as well as the acquisition of new data (phenotypic, genotypic and gene expression). PMID:22102583

Maddatu, Terry P; Grubb, Stephen C; Bult, Carol J; Bogue, Molly A

2012-01-01

302

Stackfile Database  

NASA Technical Reports Server (NTRS)

This software provides storage retrieval and analysis functionality for managing satellite altimetry data. It improves the efficiency and analysis capabilities of existing database software with improved flexibility and documentation. It offers flexibility in the type of data that can be stored. There is efficient retrieval either across the spatial domain or the time domain. Built-in analysis tools are provided for frequently performed altimetry tasks. This software package is used for storing and manipulating satellite measurement data. It was developed with a focus on handling the requirements of repeat-track altimetry missions such as Topex and Jason. It was, however, designed to work with a wide variety of satellite measurement data [e.g., Gravity Recovery And Climate Experiment -- GRACE). The software consists of several command-line tools for importing, retrieving, and analyzing satellite measurement data.

deVarvalho, Robert; Desai, Shailen D.; Haines, Bruce J.; Kruizinga, Gerhard L.; Gilmer, Christopher

2013-01-01

303

Algaline Database  

NSDL National Science Digital Library

Maintained by the Finnish Institute of Marine Research and several other institutions, the Algaline Database offers updated reports on the conditions of phytoplankton and related parameters in the Baltic Sea. The reports, which vary in length and detail (though most are brief), summarize measurements of Oxygen, Salinity, Temperature, Nutrients, Harmful substances, Plankton, Zooplankton, Benthic Animals, Flow, and Other measurements. In addition, the Maps and Figures section offers numerous color images (including satellite) of Baltic Sea conditions and marine organisms. To access reports by geographic subregion of the Baltic, head to the Reports section. Finally, the Latest News section keeps researchers abreast of changing conditions (e.g., algal blooms) and research cruises in the Baltic. For researchers or anyone else wanting in-depth information on a host of ecological parameters for the Baltic Sea, this is an excellent reference site.

304

Marginal public health gain of screening for colorectal cancer: modelling study, based on WHO and national databases in the Nordic countries  

PubMed Central

Aims To estimate the potential gain of national screening programmes for colorectal cancer (CRC) by stool occult blood testing in the Nordic countries, with comparative reference to the burden of other causes of premature death. Methods Implementation of national screening programmes for CRC was modelled among people 55–74 years in accordance with the 2011 Cochrane review of biannual screening, using the faecal occult blood test (FOBT) for 10 years, resulting in 15% relative risk reduction in CRC deaths among all those invited [intention-to-treat; relative risk 0.85; confidence interval (CI) 0.78 to 0.92]. Our calculations are based on the World Health Organization and national databanks on death causes (ICD-10) and the mid-year number of inhabitants in the target group. For Finland, Denmark, Norway and Sweden, we used data for 2009. For Iceland, due to the population's small size, we calculated mean mortality for the period 2005–2009. Results Invitation to a CRC screening programme for 10 years could influence 0.5–0.9% (95%CI 0.4–1.2) of all deaths in the age group 65–74 years. Among the remaining 99% of premature deaths, around 50% were caused by lung cancer, other lung diseases, cardiovascular diseases and accidents, with some national variations. Conclusions and implications Establishment of a screening programme for CRC for people aged 55–74 can be expected to affect only a minor proportion of all premature deaths in the Nordic setting. From a public health perspective, prioritizing preventive strategies targeting more prevalent causes of premature death may be a superior approach. PMID:22519671

Sigurdsson, Johann A; Getz, Linn; Sjönell, Göran; Vainiomäki, Paula; Brodersen, John

2013-01-01

305

Environment Australia's Online Image Database  

NSDL National Science Digital Library

Environment Australia -- Australia's Department of Environment and Heritage -- has made its extensive collection of photographs freely available for non-commercial use. Researchers and students in the environmental sciences may find this collection of well-composed, high-quality images a useful resource for presentations and publications. Users may easily search the database by keyword, general subject, and/or geographic area. Search results yield a table of thumbnail photos together with summary information for each image. Before publishing an image from the database, users must first contact Environment Australia (via provided Web form).

306

Overlap in Bibliographic Databases.  

ERIC Educational Resources Information Center

Examines the topic of Fuzzy Set Theory to determine the overlap of coverage in bibliographic databases. Highlights include examples of comparisons of database coverage; frequency distribution of the degree of overlap; records with maximum overlap; records unique to one database; intra-database duplicates; and overlap in the top ten databases

Hood, William W.; Wilson, Concepcion S.

2003-01-01

307

TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation.  

PubMed Central

Three databases that provide data on transcriptional regulation are described. TRANSFAC is a database on transcription factors and their DNA binding sites. TRRD (Transcription Regulatory Region Database) collects information about complete regulatory regions, their regulation properties and architecture. COMPEL comprises specific information on composite regulatory elements. Here, we describe the present status of these databases and the first steps towards their federation. PMID:9016550

Wingender, E; Kel, A E; Kel, O V; Karas, H; Heinemeyer, T; Dietze, P; Knüppel, R; Romaschenko, A G; Kolchanov, N A

1997-01-01

308

Database and software for the analysis of mutations at the human p53 gene.  

PubMed

A computerized database containing DNA sequence information regarding human p53 mutants has been created. The database itself is in the dBASE format and contains information on nearly 3000 mutants. In addition, an IBM PC compatible software package to analyze the information in the database has been developed. Both the database and software are freely available via the Internet. PMID:7937054

Cariello, N F; Beroud, C; Soussi, T

1994-09-01

309

Database and software for the analysis of mutations at the human hprt gene.  

PubMed

A computerized database containing DNA sequence information regarding human HPRT mutants has been created. The database itself is in the dBASE format and contains information on about 1500 mutants. In addition, an IBM PC compatible software package to analyze the information in the database has been developed. Both the database and software are freely available via the Internet. PMID:7937053

Cariello, N F

1994-09-01

310

DNA sequence comparison based on amino acid similarity  

E-print Network

DNA databases are growing exponentially. Sequence similarities are often the most valuable information we can get from DNA databases. Especially for protein-coding sequences, comparison of translated sequences give us clues to protein function. However gaps in DNA sequences prevent us from translation and force us to compare them as they are. We present an algorithm for DNA sequence comparison which translates the sequences most reliably and compares the translated sequences. The method enables us to find protein sequence similarity in DNA sequences even if we do not know the protein sequences which are coded in the DNA sequences. 1 Introduction Most of protein sequences are determined from DNA sequences. DNA database size is increasing exponentially. If we can translate all protein-coding sequences in DNA databases it will make the most up-to-date protein databases. However translation is impossible for some of the sequences because of difficulty of predicting coding regions and alte...

Hiraoka Nagai; S. Hiraoka; K. Nagai

311

WEBrary: Putting Your In-House Databases on the Web.  

ERIC Educational Resources Information Center

The WEBrary(R) databases at the Morton Grove Public Library (Illinois) provide patron-accessible searchable databases, easily available over the library's Web site. Database offerings include the locally maintained Song Collection Index, Obituary Index, Continuations Listings, On-Order files, topical and personalized New Acquisitions files, and…

Justie, Kevin M.

1999-01-01

312

16 CFR 1102.28 - Publication of reports of harm.  

Code of Federal Regulations, 2013 CFR

...AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural Requirements § 1102...the requirements for publication in the Database. The Commission will publish reports...requirements of § 1102.10(d) in the Database beyond the 10-business-day time...

2013-01-01

313

16 CFR 1102.28 - Publication of reports of harm.  

Code of Federal Regulations, 2012 CFR

...AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural Requirements § 1102...the requirements for publication in the Database. The Commission will publish reports...requirements of § 1102.10(d) in the Database beyond the 10-business-day time...

2012-01-01

314

16 CFR 1102.28 - Publication of reports of harm.  

Code of Federal Regulations, 2014 CFR

...AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural Requirements § 1102...the requirements for publication in the Database. The Commission will publish reports...requirements of § 1102.10(d) in the Database beyond the 10-business-day time...

2014-01-01

315

ASMENET Jobs Database  

NSDL National Science Digital Library

The American Society of Mechanical Engineers offers this searchable and browsable (see database search tip) database of Mechanical Engineering related jobs. The database can be searched by location, title, company, or job responsibilities.

1998-01-01

316

DNA DNA [1]. 1994  

E-print Network

1. 1) DNA DNA [1]. 1994 * Molecular Evolutionary Computing(MEC) . ** *** : DNA / : 151-742 56-1 : 02)880-1847 FAX: 02)875-2240 : {ejpark, ihlee, btzhang}@bi.snu.ac.kr (L. M. Adleman) DNA (Hamiltonian Path Problem) [2] , NP- (NP-complete) [3]. DNA

317

CEBAF Large Acceptance Spectrometer (CLAS) Physics Database  

DOE Data Explorer

A username and password are required to access and search the entire database. However, the Overview page provides links to detailed data pages for each of the experiments available for public access. There are many experiments with data that the public can freely access.

318

On-Line Databases in Mexico.  

ERIC Educational Resources Information Center

Use of online bibliographic databases in Mexico is provided through Servicio de Consulta a Bancos de Informacion, a public service that provides information retrieval, document delivery, translation, technical support, and training services. Technical infrastructure is based on a public packet-switching network and institutional users may receive…

Molina, Enzo

1986-01-01

319

Three Decades of Recombinant DNA.  

ERIC Educational Resources Information Center

Discusses highlights in the development of genetic engineering, examining techniques with recombinant DNA, legal and ethical issues, GenBank (a national database of nucleic acid sequences), and other topics. (JN)

Palmer, Jackie

1985-01-01

320

National Residential Efficiency Measures Database  

DOE Data Explorer

The National Residential Efficiency Measures Database is a publicly available, centralized resource of residential building retrofit measures and costs for the U.S. building industry. With support from the U.S. Department of Energy, NREL developed this tool to help users determine the most cost-effective retrofit measures for improving energy efficiency of existing homes. Software developers who require residential retrofit performance and cost data for applications that evaluate residential efficiency measures are the primary audience for this database. In addition, home performance contractors and manufacturers of residential materials and equipment may find this information useful. The database offers the following types of retrofit measures: 1) Appliances, 2) Domestic Hot Water, 3) Enclosure, 4) Heating, Ventilating, and Air Conditioning (HVAC), 5) Lighting, 6) Miscellaneous.

321

16 CFR 1102.30 - Publication of manufacturer comments.  

Code of Federal Regulations, 2013 CFR

...REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural Requirements § 1102.30 Publication of manufacturer...1102.24, and 1102.26, the Commission will publish in the Database manufacturer comments submitted in response to a report of...

2013-01-01

322

16 CFR 1102.30 - Publication of manufacturer comments.  

Code of Federal Regulations, 2014 CFR

...REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural Requirements § 1102.30 Publication of manufacturer...1102.24, and 1102.26, the Commission will publish in the Database manufacturer comments submitted in response to a report of...

2014-01-01

323

16 CFR 1102.30 - Publication of manufacturer comments.  

Code of Federal Regulations, 2012 CFR

...REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural Requirements § 1102.30 Publication of manufacturer...1102.24, and 1102.26, the Commission will publish in the Database manufacturer comments submitted in response to a report of...

2012-01-01

324

Mouse Phenome Database  

PubMed Central

The Mouse Phenome Database (MPD; phenome.jax.org) was launched in 2001 as the data coordination center for the international Mouse Phenome Project. MPD integrates quantitative phenotype, gene expression and genotype data into a common annotated framework to facilitate query and analysis. MPD contains >3500 phenotype measurements or traits relevant to human health, including cancer, aging, cardiovascular disorders, obesity, infectious disease susceptibility, blood disorders, neurosensory disorders, drug addiction and toxicity. Since our 2012 NAR report, we have added >70 new data sets, including data from Collaborative Cross lines and Diversity Outbred mice. During this time we have completely revamped our homepage, improved search and navigational aspects of the MPD application, developed several web-enabled data analysis and visualization tools, annotated phenotype data to public ontologies, developed an ontology browser and released new single nucleotide polymorphism query functionality with much higher density coverage than before. Here, we summarize recent data acquisitions and describe our latest improvements. PMID:24243846

Grubb, Stephen C.; Bult, Carol J.; Bogue, Molly A.

2014-01-01

325

Interactive bibliographical database on color  

NASA Astrophysics Data System (ADS)

The paper describes the methodology and results of a project under development, aimed at the elaboration of an interactive bibliographical database on color in all fields of application: philosophy, psychology, semiotics, education, anthropology, physical and natural sciences, biology, medicine, technology, industry, architecture and design, arts, linguistics, geography, history. The project is initially based upon an already developed bibliography, published in different journals, updated in various opportunities, and now available at the Internet, with more than 2,000 entries. The interactive database will amplify that bibliography, incorporating hyperlinks and contents (indexes, abstracts, keywords, introductions, or eventually the complete document), and devising mechanisms for information retrieval. The sources to be included are: books, doctoral dissertations, multimedia publications, reference works. The main arrangement will be chronological, but the design of the database will allow rearrangements or selections by different fields: subject, Decimal Classification System, author, language, country, publisher, etc. A further project is to develop another database, including color-specialized journals or newsletters, and articles on color published in international journals, arranged in this case by journal name and date of publication, but allowing also rearrangements or selections by author, subject and keywords.

Caivano, Jose L.

2002-06-01

326

Creating a Serial Database Using Subscription Agency Files  

Microsoft Academic Search

Subscription agency invoice files on diskette can be transferred into standard microcomputer database management packages to provide libraries with a fast low-cost serials database useful for various public or technical service functions and for management decision-making. Specific procedures are detailed for producing such a database using EBSCO Subscription Services invoice diskettes and the PC-File III and dBASE III PLUS database

Susan A. Cady

1988-01-01

327

Saudi Arabian National Center for Science and Technology (SANCST) Database.  

ERIC Educational Resources Information Center

Subject areas covered by publications in database of Saudi Arabian National Center for Science and Technology are enumerated, noting Saudi contribution: total number of publications in individual subject areas, number of publications for each area and year, and publication trends (1960-1982). Scientific and technological activities in Saudi Arabia…

Manzoor, Suhail

1985-01-01

328

Curation accuracy of model organism databases  

PubMed Central

Manual extraction of information from the biomedical literature—or biocuration—is the central methodology used to construct many biological databases. For example, the UniProt protein database, the EcoCyc Escherichia coli database and the Candida Genome Database (CGD) are all based on biocuration. Biological databases are used extensively by life science researchers, as online encyclopedias, as aids in the interpretation of new experimental data and as golden standards for the development of new bioinformatics algorithms. Although manual curation has been assumed to be highly accurate, we are aware of only one previous study of biocuration accuracy. We assessed the accuracy of EcoCyc and CGD by manually selecting curated assertions within randomly chosen EcoCyc and CGD gene pages and by then validating that the data found in the referenced publications supported those assertions. A database assertion is considered to be in error if that assertion could not be found in the publication cited for that assertion. We identified 10 errors in the 633 facts that we validated across the two databases, for an overall error rate of 1.58%, and individual error rates of 1.82% for CGD and 1.40% for EcoCyc. These data suggest that manual curation of the experimental literature by Ph.D-level scientists is highly accurate. Database URL: http://ecocyc.org/, http://www.candidagenome.org// PMID:24923819

Keseler, Ingrid M.; Skrzypek, Marek; Weerasinghe, Deepika; Chen, Albert Y.; Fulcher, Carol; Li, Gene-Wei; Lemmer, Kimberly C.; Mladinich, Katherine M.; Chow, Edmond D.; Sherlock, Gavin; Karp, Peter D.

2014-01-01

329

The UCSC Genome Browser database: 2015 update.  

PubMed

Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (http://genome.ucsc.edu) and associated tools continue to grow, providing a comprehensive resource of genome assemblies and annotations to scientists and students worldwide. Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation (100-species multiple alignment and conservation) and a novel distribution mechanism for the browser (GBiB: Genome Browser in a Box). We created browsers for new species (Chinese hamster, elephant shark, minke whale), 'mined the web' for DNA sequences and expanded the browser display with stacked color graphs and region highlighting. As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data hubs has tripled. PMID:25428374

Rosenbloom, Kate R; Armstrong, Joel; Barber, Galt P; Casper, Jonathan; Clawson, Hiram; Diekhans, Mark; Dreszer, Timothy R; Fujita, Pauline A; Guruvadoo, Luvina; Haeussler, Maximilian; Harte, Rachel A; Heitner, Steve; Hickey, Glenn; Hinrichs, Angie S; Hubley, Robert; Karolchik, Donna; Learned, Katrina; Lee, Brian T; Li, Chin H; Miga, Karen H; Nguyen, Ngan; Paten, Benedict; Raney, Brian J; Smit, Arian F A; Speir, Matthew L; Zweig, Ann S; Haussler, David; Kuhn, Robert M; Kent, W James

2015-01-28

330

Privacy-Preserving Matching of DNA Profiles Fons Bruekers1  

E-print Network

Privacy-Preserving Matching of DNA Profiles Fons Bruekers1 , Stefan Katzenbeisser1,2 , Klaus a commodity. Most western governments keep databases with DNA profiles of criminal offenders and suspects profiles; the British authorities alone maintain a database containing DNA samples of more than five per

331

Current trends in publicly available genetic databases  

Microsoft Academic Search

Analysis of human genetic data promises to uncover important disease targets. Genes known to cause or increase susceptibility for various diseases are being identified through analysis of genetic data, expression and metabolites. Future benefits to individuals are far-reaching, including improved gene therapy strategies, better drug development for disease treatment, pre-symptomatic disease intervention and risk susceptibility information. The rapid expansion of

Michael G. Tyshenko; William Leiss

2005-01-01

332

DNA Barcoding for Species Assignment: The Case of Mediterranean Marine Fishes  

PubMed Central

Background DNA barcoding enhances the prospects for species-level identifications globally using a standardized and authenticated DNA-based approach. Reference libraries comprising validated DNA barcodes (COI) constitute robust datasets for testing query sequences, providing considerable utility to identify marine fish and other organisms. Here we test the feasibility of using DNA barcoding to assign species to tissue samples from fish collected in the central Mediterranean Sea, a major contributor to the European marine ichthyofaunal diversity. Methodology/Principal Findings A dataset of 1278 DNA barcodes, representing 218 marine fish species, was used to test the utility of DNA barcodes to assign species from query sequences. We tested query sequences against 1) a reference library of ranked DNA barcodes from the neighbouring North East Atlantic, and 2) the public databases BOLD and GenBank. In the first case, a reference library comprising DNA barcodes with reliability grades for 146 fish species was used as diagnostic dataset to screen 486 query DNA sequences from fish specimens collected in the central basin of the Mediterranean Sea. Of all query sequences suitable for comparisons 98% were unambiguously confirmed through complete match with reference DNA barcodes. In the second case, it was possible to assign species to 83% (BOLD-IDS) and 72% (GenBank) of the sequences from the Mediterranean. Relatively high intraspecific genetic distances were found in 7 species (2.2%–18.74%), most of them of high commercial relevance, suggesting possible cryptic species. Conclusion/Significance We emphasize the discriminatory power of COI barcodes and their application to cases requiring species level resolution starting from query sequences. Results highlight the value of public reference libraries of reliability grade-annotated DNA barcodes, to identify species from different geographical origins. The ability to assign species with high precision from DNA samples of disparate quality and origin has major utility in several fields, from fisheries and conservation programs to control of fish products authenticity. PMID:25222272

Landi, Monica; Dimech, Mark; Arculeo, Marco; Biondo, Girolama; Martins, Rogelia; Carneiro, Miguel; Carvalho, Gary Robert; Brutto, Sabrina Lo; Costa, Filipe O.

2014-01-01

333

Database Management Certificate Program  

E-print Network

Database Management Certificate Program DATABASE TECHNOLOGIES 13 Today, organizations in every to obtain general data analysis and management skills or apply both Oracle and Microsoft SQL Server database capabilities of relational databases in conjunction with the new "Big Data" management frameworks for data

Rose, Michael R.

334

Reflective Database Access Control  

ERIC Educational Resources Information Center

"Reflective Database Access Control" (RDBAC) is a model in which a database privilege is expressed as a database query itself, rather than as a static privilege contained in an access control list. RDBAC aids the management of database access controls by improving the expressiveness of policies. However, such policies introduce new interactions…

Olson, Lars E.

2009-01-01

335

DNA Sequencing apparatus  

DOEpatents

An automated DNA sequencing apparatus having a reactor for providing at least two series of DNA products formed from a single primer and a DNA strand, each DNA product of a series differing in molecular weight and having a chain terminating agent at one end; separating means for separating the DNA products to form a series bands, the intensity of substantially all nearby bands in a different series being different, band reading means for determining the position an This invention was made with government support including a grant from the U.S. Public Health Service, contract number AI-06045. The U.S. government has certain rights in the invention.

Tabor, Stanley (Cambridge, MA); Richardson, Charles C. (Chestnut Hill, MA)

1992-01-01

336

The Organelle Genome Database Project (GOBASE).  

PubMed Central

The taxonomically broad organelle genome database (GOBASE) organizes and integrates diverse data related to organelles (mitochondria and chloroplasts). The current version of GOBASE focuses on the mitochondrial subset of data and contains molecular sequences, RNA secondary structures and genetic maps, as well as taxonomic information for all eukaryotic species represented. The database has been designed so that complex biological queries, especially ones posed in a comparative genomics context, are supported. GOBASE has been implemented as a relational database with a web-based user interface (http://megasun.bch.umontreal.ca/gobase/gobas e.html ). Custom software tools have been written in house to assist in the population of the database, data validation, nomenclature standardization and front-end design. The database is fully operational and publicly accessible via the World Wide Web, allowing interactive browsing, sophisticated searching and easy downloading of data. PMID:9399818

Korab-Laskowska, M; Rioux, P; Brossard, N; Littlejohn, T G; Gray, M W; Lang, B F; Burger, G

1998-01-01

337

Silicon Valley Companies Database (SV150)  

NSDL National Science Digital Library

Created by Mercury Center, the online service of the San Jose Mercury News, this database offers financial information and company background for the 150 largest publicly traded companies in Silicon Valley. Silicon Valley is defined as the cities of Santa Cruz and Santa Clara, as well as the southern sections of San Mateo and Alameda counties. The database is searchable by company name, stock symbol, 1997 sales, industry type, product, and location. Clear, detailed instructions will help users best use the database. The search results link to company homepages and charted stock prices.

338

University of Washington: Database Research Group  

NSDL National Science Digital Library

The University of Washington's Database Research Group âÂÂis focused on broadening the scope of database and data management techniques beyond their traditional scope.â Its work focuses on databases and the Web, XML, data management for ubiquitous computing, data integration, and data mining. For example, the Mangrove project seeks to facilitate the move to the semantic Web by creating âÂÂan environment in which users are motivated to create semantic content because of the existence of useful semantic services.â The various projects are described on this website along with related publications, which are available to download.

339

YMDB: the Yeast Metabolome Database.  

PubMed

The Yeast Metabolome Database (YMDB, http://www.ymdb.ca) is a richly annotated 'metabolomic' database containing detailed information about the metabolome of Saccharomyces cerevisiae. Modeled closely after the Human Metabolome Database, the YMDB contains >2000 metabolites with links to 995 different genes/proteins, including enzymes and transporters. The information in YMDB has been gathered from hundreds of books, journal articles and electronic databases. In addition to its comprehensive literature-derived data, the YMDB also contains an extensive collection of experimental intracellular and extracellular metabolite concentration data compiled from detailed Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) metabolomic analyses performed in our lab. This is further supplemented with thousands of NMR and MS spectra collected on pure, reference yeast metabolites. Each metabolite entry in the YMDB contains an average of 80 separate data fields including comprehensive compound description, names and synonyms, structural information, physico-chemical data, reference NMR and MS spectra, intracellular/extracellular concentrations, growth conditions and substrates, pathway information, enzyme data, gene/protein sequence data, as well as numerous hyperlinks to images, references and other public databases. Extensive searching, relational querying and data browsing tools are also provided that support text, chemical structure, spectral, molecular weight and gene/protein sequence queries. Because of S. cervesiae's importance as a model organism for biologists and as a biofactory for industry, we believe this kind of database could have considerable appeal not only to metabolomics researchers, but also to yeast biologists, systems biologists, the industrial fermentation industry, as well as the beer, wine and spirit industry. PMID:22064855

Jewison, Timothy; Knox, Craig; Neveu, Vanessa; Djoumbou, Yannick; Guo, An Chi; Lee, Jacqueline; Liu, Philip; Mandal, Rupasri; Krishnamurthy, Ram; Sinelnikov, Igor; Wilson, Michael; Wishart, David S

2012-01-01

340

Genotype-based databases for variants causing rare diseases.  

PubMed

Inherited diseases are the result of DNA sequence changes. In recessive diseases, the clinical phenotype results from the combined functional effects of variants in both copies of the gene. In some diseases there is often considerable variability of clinical presentation or disease severity, which may be predicted by the genotype. Additional effects may be triggered by environmental factors, as well as genetic modifiers which could be nucleotide polymorphisms in related genes, e.g. maternal ApoE or ABCA1 genotypes which may have an influence on the phenotype of SLOS individuals. Here we report the establishment of genotype variation databases for various rare diseases which provide individual clinical phenotypes associated with genotypes and include data about possible genetic modifiers. These databases aim to be an easy public access to information on rare and private variants with clinical data, which will facilitate the interpretation of genetic variants. The created databases include ACAD8 (isobutyryl-CoA dehydrogenase deficiency (IBD)), ACADSB (short-chain acyl-CoA dehydrogenase (SCAD) deficiency), AUH (3-methylglutaconic aciduria (3-MGCA)), DHCR7 (Smith-Lemli-Opitz syndrome), HMGCS2 (3-hydroxy-3-methylglutaryl-CoA synthase 2 deficiency), HSD17B10 (17-beta-hydroxysteroid dehydrogenase X deficiency), FKBP14 (Ehlers-Danlos syndrome with progressive kyphoscoliosis, myopathy, and hearing loss; EDSKMH) and ROGDI (Kohlschütter-Tönz syndrome). These genes have been selected because of our specific research interests in these rare and metabolic diseases. The aim of the database was to include all identified individuals with variants in these specific genes. Identical genotypes are listed multiple times if they were found in several patients, phenotypic descriptions and biochemical data are included as detailed as possible in view also of validating the proposed pathogenicity of these genotypes. For DHCR7 genetic modifier data (maternal APOE and ABCA1 genotypes) is also included. Databases are available at http://databases.lovd.nl/shared/genes and will be updated based on periodic literature reviews and submitted reports. PMID:25111118

Lanthaler, Barbara; Wieser, Stefanie; Deutschmann, Andrea; Schossig, Anna; Fauth, Christine; Zschocke, Johannes; Witsch-Baumgartner, Martina

2014-10-15

341

Information storage in DNA sequences  

SciTech Connect

We seek to describe a starting point for modeling the evolution of DNA sequences within the framework of cellular automata by discussing the current understanding of genetic information storage in DNA sequences. This includes alternately viewing the role of DNA in living organisms as a simple scheme and as a complex scheme; a presentation of the extent of experimentally determined DNA sequence data present in the Los Alamos Nucleic Acid Database; and finally, a brief review of strategies for identifying and classifying patterns in DNA sequences.

Burks, C.

1983-01-01

342

Reviewing population studies for forensic purposes: Dog mitochondrial DNA  

PubMed Central

Abstract The identification of dog hair through mtDNA analysis has become increasingly important in the last 15 years, as it can provide associative evidence connecting victims and suspects. The evidential value of an mtDNA match between dog hair and its potential donor is determined by the random match probability of the haplotype. This probability is based on the haplotype’s population frequency estimate. Consequently, implementing a population study representative of the population relevant to the forensic case is vital to the correct evaluation of the evidence. This paper reviews numerous published dog mtDNA studies and shows that many of these studies vary widely in sampling strategies and data quality. Therefore, several features influencing the representativeness of a population sample are discussed. Moreover, recommendations are provided on how to set up a dog mtDNA population study and how to decide whether or not to include published data. This review emphasizes the need for improved dog mtDNA population data for forensic purposes, including targeting the entire mitochondrial genome. In particular, the creation of a publicly available database of qualitative dog mtDNA population studies would improve the genetic analysis of dog traces in forensic casework. PMID:24453568

Verscheure, Sophie; Backeljau, Thierry; Desmyter, Stijn

2013-01-01

343

Reviewing population studies for forensic purposes: Dog mitochondrial DNA.  

PubMed

The identification of dog hair through mtDNA analysis has become increasingly important in the last 15 years, as it can provide associative evidence connecting victims and suspects. The evidential value of an mtDNA match between dog hair and its potential donor is determined by the random match probability of the haplotype. This probability is based on the haplotype's population frequency estimate. Consequently, implementing a population study representative of the population relevant to the forensic case is vital to the correct evaluation of the evidence. This paper reviews numerous published dog mtDNA studies and shows that many of these studies vary widely in sampling strategies and data quality. Therefore, several features influencing the representativeness of a population sample are discussed. Moreover, recommendations are provided on how to set up a dog mtDNA population study and how to decide whether or not to include published data. This review emphasizes the need for improved dog mtDNA population data for forensic purposes, including targeting the entire mitochondrial genome. In particular, the creation of a publicly available database of qualitative dog mtDNA population studies would improve the genetic analysis of dog traces in forensic casework. PMID:24453568

Verscheure, Sophie; Backeljau, Thierry; Desmyter, Stijn

2013-12-30

344

ECD--a totally integrated database of Escherichia coli K12.  

PubMed Central

We have compiled the DNA sequence data for E. coli available from the GENBANK and EMBL data libraries and independently from the literature. Starting with this update of our Escherichia coli database (ECD release 20) we provide major changes compared to previous issues. This update not only represents another substantial increase in sequence information, it also allows now to find the exact physical location of each individual gene or regulatory region, even regarding discrepancies in nomenclature. In order to save space this printed version does not contain the database itself anymore, but we provide several examples. The complete database is publically available in electronic form together with a self explaining application program or as a flat file. The complete compilation including a full set of genetic map data and the E. coli protein index can be obtained in machine readable form from the EMBL data library as a part of the CD-ROM issue of the EMBL sequence database, released and updated every three months. After deletion of all detected overlaps a total of 2,878,364 individual bp is found to be determined till the end of June 1994. This corresponds to a total of 60.98% of the entire E. coli chromosome consisting of about 4,720 kbp. This number may actually be higher by 9161 bp derived from other strains of E. coli. PMID:7937044

Wahl, R; Rice, P; Rice, C M; Kröger, M

1994-01-01

345

Cancer Control Publications 1998-2011: About CC Publications  

Cancer.gov

The Division of Cancer Control and Population Sciences (DCCPS) funds over 900 grants annually. CC Publications is a searchable database that highlights publications resulting from DCCPS-funded research and staff research findings. These publications have been retrieved through PubMed, grants final reports, and staff reporting.

346

The EMIME Bilingual Database   

E-print Network

This paper describes the collection of a bilingual database of Finnish/English and German/English data. In addition, the accents of the talkers in the database have been rated. English, German and Finnish listeners assessed the English, German...

Wester, Mirjam

2010-01-01

347

Household Products Database: Pesticides  

MedlinePLUS

... Names Types of Products Manufacturers Ingredients About the Database FAQ Product Recalls Help Glossary Contact Us More ... holders. Information is extracted from Consumer Product Information Database ©2001-2014 by DeLima Associates. All rights reserved. ...

348

NIOSH Power Tools Database  

MedlinePLUS

... Search Tool Type: Manufacturer: Technical Specifications: Power Tools Database Choose one of the tools below to view sound specifications. Disclaimer: The NIOSH database does not include a comprehensive list of manufacturers ...

349

Search the PAQ Database  

Cancer.gov

Use this interface to search through all the physical activity-related questions in our database. See below for some tips on how to search. If you have any comments concerning this database, please e-mail David Berrigan.

350

ECOTOX DATABASE SYSTEM  

EPA Science Inventory

The ECOTOXicology database is a source for locating single chemical toxicity data for aquatic life, terrestrial plants and wildlife. ECOTOX integrates three toxicology effects databases: AQUIRE (aquatic life), PHYTOTOX (terrestrial plants), and TERRETOX (terrestrial wildlife). Th...

351

THE ECOTOX DATABASE  

EPA Science Inventory

The database provides chemical-specific toxicity information for aquatic life, terrestrial plants, and terrestrial wildlife. ECOTOX is a comprehensive ecotoxicology database and is therefore essential for providing and suppoirting high quality models needed to estimate population...

352

Structural Ceramics Database  

National Institute of Standards and Technology Data Gateway

SRD 30 NIST Structural Ceramics Database (Web, free access)   The NIST Structural Ceramics Database (WebSCD) provides evaluated materials property data for a wide range of advanced ceramics known variously as structural ceramics, engineering ceramics, and fine ceramics.

353

The Database Index.  

ERIC Educational Resources Information Center

Describes the characteristics of System Development Corporation's (SDC) online index to its database, "Database Index," and presents the results of various test searches to demonstrate the limitations and benefits of the new online file. (JD)

Antony, Arthur

1979-01-01

354

Physiological Information Database (PID)  

EPA Science Inventory

EPA has developed a physiological information database (created using Microsoft ACCESS) intended to be used in PBPK modeling. The database contains physiological parameter values for humans from early childhood through senescence as well as similar data for laboratory animal spec...

355

An occurence records database of French Guiana harvestmen (Arachnida, Opiliones)  

PubMed Central

Abstract This dataset provides information on specimens of harvestmen (Arthropoda, Arachnida, Opiliones) collected in French Guiana. Field collections have been initiated in 2012 within the framework of the CEnter for the Study of Biodiversity in Amazonia (CEBA: www.labex-ceba.fr/en/). This dataset is a work in progress.  Occurrences are recorded in an online database stored at the EDB laboratory after each collecting trip and the dataset is updated on a monthly basis. Voucher specimens and associated DNA are also stored at the EDB laboratory until deposition in natural history Museums. The latest version of the dataset is publicly and freely accessible through our Integrated Publication Toolkit at http://130.120.204.55:8080/ipt/resource.do?r=harvestmen_of_french_guiana or through the Global Biodiversity Information Facility data portal at http://www.gbif.org/dataset/3c9e2297-bf20-4827-928e-7c7eefd9432c. PMID:25589875

Solbès, Pierre; Grosso, Bernadette

2014-01-01

356

NASA scientific and technical publications: A catalog of special publications, reference publications, conference publications, and technical papers, 1991-1992  

NASA Technical Reports Server (NTRS)

This catalog lists 458 citations of all NASA Special Publications, NASA Reference Publications, NASA Conference Publications, and NASA Technical Papers that were entered into the NASA Scientific and Technical Information database during accession year 1991 through 1992. The entries are grouped by subject category. Indexes of subject terms, personal authors, and NASA report numbers are provided.

1993-01-01

357

NASA scientific and technical publications: A catalog of special publications, reference publications, conference publications, and technical papers, 1989  

NASA Technical Reports Server (NTRS)

This catalog lists 190 citations of all NASA Special Publications, NASA Reference Publications, NASA Conference Publications, and NASA Technical Papers that were entered into the NASA scientific and technical information database during accession year 1989. The entries are grouped by subject category. Indexes of subject terms, personal authors, and NASA report numbers are provided.

1990-01-01

358

NASA scientific and technical publications: A catalog of Special Publications, Reference Publications, Conference Publications, and Technical Papers, 1987  

NASA Technical Reports Server (NTRS)

This catalog lists 239 citations of all NASA Special Publications, NASA Reference Publications, NASA Conference Publications, and NASA Technical Papers that were entered in the NASA scientific and technical information database during accession year 1987. The entries are grouped by subject category. Indexes of subject terms, personal authors, and NASA report numbers are provided.

1988-01-01

359

NASA scientific and technical publications: A catalog of special publications, reference publications, conference publications, and technical papers, 1987-1990  

NASA Technical Reports Server (NTRS)

This catalog lists 783 citations of all NASA Special Publications, NASA Reference Publications, NASA Conference Publications, and NASA Technical Papers that were entered into NASA Scientific and Technical Information Database during the year's 1987 through 1990. The entries are grouped by subject category. Indexes of subject terms, personal authors, and NASA report numbers are provided.

1991-01-01

360

The MRC psycholinguistic database  

Microsoft Academic Search

This paper describes a computerised database of psycholinguistic information. Semantic, syntactic, phonological and orthographic information about some or all of the 98,538 words in the database is accessible, by using a specially-written and very simple programming language. Word-association data are also included in the database. Some examples are given of the use of the database for selection of stimuli to

Max Coltheart

1981-01-01

361

DHQ Database Revision History  

Cancer.gov

The following details all additions and revisions made to the DHQ nutrient and food database. This revision history is provided as a reference for investigators who may have performed analyses with a previous release of the database. The contents of the current database are listed in Nutrient and Dietary Constituents and Pyramid Food Groups.

362

Database Encryption Luc Bouganim  

E-print Network

Database Encryption Luc Bouganim INRIA Rocquencourt Le Chesnay, FRANCE Luc.Bouganim@inria.fr Yanli GUO INRIA Rocquencourt Le Chesnay, FRANCE yanli.guo@inria.fr Related concepts and keywords Database security, Data confidentiality, Hardware Security Module Definition Database encryption refers to the use

Paris-Sud XI, Université de

363

USER'S GUIDE DATABASE SYSTEM  

E-print Network

USER'S GUIDE TO THE MINGL DATABASE SYSTEM FOR TFTR Version 4.1 R. M. Wieland Plasma Physics blank] #12;1 Abstract The MINGL database system is an integrated set of tools which is used to collect relational databases. A flexible software tool set makes it easy to browse, select, compare and display

364

ORACLE CERTIFICATION Oracle Database  

E-print Network

ORACLE CERTIFICATION Oracle Database Administration Certificate Program Train with the best. Get your Oracle Database Administration education from the number-one provider* of Oracle training-on, lab-based understanding of Oracle, the world's leading database platform, and long the product

Loudon, Catherine

365

Mission and Assets Database  

NASA Technical Reports Server (NTRS)

Mission and Assets Database (MADB) Version 1.0 is an SQL database system with a Web user interface to centralize information. The database stores flight project support resource requirements, view periods, antenna information, schedule, and forecast results for use in mid-range and long-term planning of Deep Space Network (DSN) assets.

Baldwin, John; Zendejas, Silvino; Gutheinz, Sandy; Borden, Chester; Wang, Yeou-Fang

2009-01-01

366

The Columbia grasp database  

Microsoft Academic Search

Collecting grasp data for learning and bench- marking purposes is very expensive. It would be helpful to have a standard database of graspable objects, along with a set of stable grasps for each object, but no such database exists. In this work we show how to automate the construction of a database consisting of several hands, thousands of objects, and

Corey Goldfeder; Matei T. Ciocarlie; Hao Dang; Peter K. Allen

2009-01-01

367

Database extraction strategies for low-template evidence.  

PubMed

Often in forensic cases, the profile of at least one of the contributors to a DNA evidence sample is unknown and a database search is needed to discover possible perpetrators. In this article we consider two types of search strategies to extract suspects from a database using methods based on probability arguments. The performance of the proposed match scores is demonstrated by carrying out a study of each match score relative to the level of allele drop-out in the crime sample, simulating low-template DNA. The efficiency was measured by random man simulation and we compared the performance using the SGM Plus kit and the ESX 17 kit for the Norwegian population, demonstrating that the latter has greatly enhanced power to discover perpetrators of crime in large national DNA databases. The code for the database extraction strategies will be prepared for release in the R-package forensim. PMID:24528591

Bleka, Øyvind; Dørum, Guro; Haned, Hinda; Gill, Peter

2014-03-01

368

GOLD: The Genomes Online Database  

DOE Data Explorer

Since its inception in 1997, GOLD has continuously monitored genome sequencing projects worldwide and has provided the community with a unique centralized resource that integrates diverse information related to Archaea, Bacteria, Eukaryotic and more recently Metagenomic sequencing projects. As of September 2007, GOLD recorded 639 completed genome projects. These projects have their complete sequence deposited into the public archival sequence databases such as GenBank EMBL,and DDBJ. From the total of 639 complete and published genome projects as of 9/2007, 527 were bacterial, 47 were archaeal and 65 were eukaryotic. In addition to the complete projects, there were 2158 ongoing sequencing projects. 1328 of those were bacterial, 59 archaeal and 771 eukaryotic projects. Two types of metadata are provided by GOLD: (i) project metadata and (ii) organism/environment metadata. GOLD CARD pages for every project are available from the link of every GOLD_STAMP ID. The information in every one of these pages is organized into three tables: (a) Organism information, (b) Genome project information and (c) External links. [The Genomes On Line Database (GOLD) in 2007: Status of genomic and metagenomic projects and their associated metadata, Konstantinos Liolios, Konstantinos Mavromatis, Nektarios Tavernarakis and Nikos C. Kyrpides, Nucleic Acids Research Advance Access published online on November 2, 2007, Nucleic Acids Research, doi:10.1093/nar/gkm884]

The basic tables in the GOLD database that can be browsed or searched include the following information:

  • Gold Stamp ID
  • Organism name
  • Domain
  • Links to information sources
  • Size and link to a map, when available
  • Chromosome number, Plas number, and GC content
  • A link for downloading the actual genome data
  • Institution that did the sequencing
  • Funding source
  • Database where information resides
  • Publication status and information

(Specialized Interface)

Kyrpides, Nikos; Liolios, Dinos; Chen, Amy; Tavernarakis, Nektarios; Hugenholtz, Philip; Markowitz, Victor; Bernal, Alex

369

Comprehensive Thematic T-matrix Reference Database: a 2013-2014 Update  

NASA Technical Reports Server (NTRS)

This paper is the sixth update to the comprehensive thematic database of peer-reviewedT-matrix publications initiated by us in 2004 and includes relevant publications that have appeared since 2013. It also lists several earlier publications not incorporated in the original database and previous updates.

Mishchenko, Michael I.; Zakharova, Nadezhda T.; Khlebtsov, Nikolai G.; Wriedt, Thomas; Videen, Gorden

2014-01-01

370

Space medicine research publications: 1983-1984  

NASA Technical Reports Server (NTRS)

A list of publications supported by the Space Medicine Program, Office of Space Science and Applications is given. Included are publications entered into the Life Sciences Bibliographic Database by The George Washington University as of October 1, 1984.

Solberg, J. L.; Pleasant, L. G.

1984-01-01

371

ETC Spills Technology Databases: Oil Properties Database  

NSDL National Science Digital Library

The Environmental Technology Center of Environment Canada provides a database which contains various properties of crude oils and petroleum products. In addition to the listing of oils, the database reports properties "which will likely determine the environmental behavior and effects of spilled oil." The user may select an oil from a pull-down menu that lists 412 oils. The data are organized into tables in the following areas: Origin, API Gravity, Density, Pour Point, Dynamic Viscosity, Hydrocarbon Groups, and Distillation.

Fieldhouse, B.; Fingas, M.; Jokuty, P.; Lambert, P.; Mullin, J.; Wang, Z.

372

DOLOP: A Database of Bacterial Lipoproteins  

NSDL National Science Digital Library

Bacteria rely on protein-lipid combinations known as lipoproteins to glom onto surfaces, sense their surroundings, slurp up nutrients, shuttle DNA to other cells, and perform other life tasks. Researchers can analyze more than 270 of the molecules at DOLOP, a database from the Medical Research Council Laboratory of Molecular Biology in Cambridge, U.K. Entries describe each protein, indicate its size and function, and provide links to the Swiss-Prot database, where you can parse the molecule's sequence and structural features. The site also explains the synthesis of lipoproteins and describes the lipobox, a characteristic amino acid string to which lipids attach.

M. Maden Babu (MRC-Laboratory of Molecular Biology, Cambridge;); K. Sankaran (Centre for Biotechnology, Anna University, Chennai ;)

2001-09-15

373

Public Speaking  

NSDL National Science Digital Library

In this lesson students will evaluate famous speeches in order to identify the ways in which the speech was effective or ineffective. We will explore several websites, which present themselves as databases holding hundreds of speeches. Students will also view a video identifying ways to overcome fear of public speaking. Students will look over the websites and choose one video recorded speech from each website to go back and watch. They will then view the last website, which will remind students of what they should be looking in each type of speech. After being reminded of the qualities of each type of speech, students will be given a chart to fill out. Students will then go back to each website and view the videos which they have previouisly chosen. As students watch the speeches, they will note the ways in which the speaker meets the requirements for a quality speech, i.e. eye contact, number of vocal fillers used, vocal pitch, appearance, etc. They will record this information of their charts. First let's learn about American Rhetoric Now let's take a look at this film on conquering fear of public speaking Conquering Fear of Public Speaking Now let's take a look at Speaking Now let's take a look at Speech Club Now let's take a look at Study Great Speaches Now let's take a look at Study Sphere Public Speaking ...

Ms.maxwell

2011-10-27

374

Database tool ASGARD: an open-access database of  

E-print Network

Database tool ASGARD: an open-access database of annotated transcriptomes for emerging model database, the Assembled Searchable Giant Arthropod Read Database (ASGARD). This database is a repository include search term auto-completion sug- gestions based on database content, the ability to download

Extavour, Cassandra

375

Testing Database-Centric Applications For Causes of Database Deadlocks  

E-print Network

Testing Database-Centric Applications For Causes of Database Deadlocks Mark Grechanik, B. M. Mainul--Many organizations deploy applications that use databases by sending Structured Query Language (SQL) state- ments the same databases concurrently, database deadlocks routinely occur in these databases. Testing

Grechanik, Mark

376

Database Description with SDM: A Semantic Database Model  

E-print Network

Database Description with SDM: A Semantic Database Model MICHAEL HAMMER Massachusetts Institute of Technology and DENNIS McLEOD University of Southern California SDM is a high-level semantics-based database description and structuring formalism (database model) for databases. This database model is designed

McLeod, Dennis

377

Database description with SDM: a semantic database model  

Microsoft Academic Search

SDM is a high-level semantics-based database description and structuring formalism (database model) for databases. This database model is designed to capture more of the meaning of an application environment than is possible with contemporary database models. An SDM specification describes a database in terms of the kinds of entities that exist in the application environment, the classifications and groupings of

Michael M. Hammer; Dennis Mc Leod

1981-01-01

378

Women in Politics: Bibliographic Database  

NSDL National Science Digital Library

This bibliographic database currently holds 650 titles of recent works concerned with women in politics. A new addition to the Inter-Parliamentary Union's "Democracy through Partnership between Men and Women in Politics" site, "it provides bibliographic references to books, reports and journal articles on all aspects of women's participation in political life worldwide." The search mechanism allows users to specify type of document, geographic region, publishing organization, subject matter, author, title of periodical, and year of publication. Alternatively, there is also a subject keyword search. For more information about the Inter-Parliamentary Union Website, see the December 12, 1997 Scout Report.

379

Using the Proteomics Identifications Database (PRIDE).  

PubMed

The Proteomics Identifications Database (PRIDE) is a public data repository designed to store, disseminate, and analyze mass spectrometry based proteomics datasets. The PRIDE database can accommodate any level of detailed metadata about the submitted results, which can be queried, explored, viewed, or downloaded via the PRIDE Web interface. The PRIDE database also provides a simple, yet powerful, access control mechanism that fully supports confidential peer-reviewing of data related to a manuscript, ensuring that these results remain invisible to the general public while allowing referees and journal editors anonymized access to the data. This unit describes in detail the functionality that PRIDE provides with regards to searching, viewing, and comparing the available data, as well as different options for submitting data to PRIDE. PMID:18428683

Martens, Lennart; Jones, Phil; Côté, Richard

2008-03-01

380

The Combined Health Information Database (CHD) Online  

NSDL National Science Digital Library

A joint project of the National Institutes of Health and the Centers for Disease Control and Prevention, this unified database of bibliographic records has been available to the public since 1985, and now sports a clean new interface. There are sixteen separately maintained databases that can be searched individually or at once, ranging from AIDS Education and Alzheimers Disease to Cancer Prevention and Weight Control. The simple search interface offers a single box into which keywords are entered. The detailed search interface allows the user to specify date of publication, media type, and language, and provides multiple query boxes that may be linked together by Boolean operators. Searches return lists of matches, from which individual bibliographic records (including abstracts) may be viewed. Reprint ordering procedures are also listed. Users may also browse information on the scope and coverage of each of the sixteen databases.

1997-01-01

381

MUBII-TB-DB: a database of mutations associated with antibiotic resistance in Mycobacterium tuberculosis  

PubMed Central

Background Tuberculosis is an infectious bacterial disease caused by Mycobacterium tuberculosis. It remains a major health threat, killing over one million people every year worldwide. An early antibiotic therapy is the basis of the treatment, and the emergence and spread of multidrug and extensively drug-resistant mutant strains raise significant challenges. As these bacteria grow very slowly, drug resistance mutations are currently detected using molecular biology techniques. Resistance mutations are identified by sequencing the resistance-linked genes followed by a comparison with the literature data. The only online database is the TB Drug Resistance Mutation database (TBDReaM database); however, it requires mutation detection before use, and its interrogation is complex due to its loose syntax and grammar. Description The MUBII-TB-DB database is a simple, highly structured text-based database that contains a set of Mycobacterium tuberculosis mutations (DNA and proteins) occurring at seven loci: rpoB, pncA, katG; mabA(fabG1)-inhA, gyrA, gyrB, and rrs. Resistance mutation data were extracted after the systematic review of MEDLINE referenced publications before March 2013. MUBII analyzes the query sequence obtained by PCR-sequencing using two parallel strategies: i) a BLAST search against a set of previously reconstructed mutated sequences and ii) the alignment of the query sequences (DNA and its protein translation) with the wild-type sequences. The post-treatment includes the extraction of the aligned sequences together with their descriptors (position and nature of mutations). The whole procedure is performed using the internet. The results are graphs (alignments) and text (description of the mutation, therapeutic significance). The system is quick and easy to use, even for technicians without bioinformatics training. Conclusion MUBII-TB-DB is a structured database of the mutations occurring at seven loci of major therapeutic value in tuberculosis management. Moreover, the system provides interpretation of the mutations in biological and therapeutic terms and can evolve by the addition of newly described mutations. Its goal is to provide easy and comprehensive access through a client–server model over the Web to an up-to-date database of mutations that lead to the resistance of M. tuberculosis to antibiotics. PMID:24731071

2014-01-01

382

The EMBL Nucleotide Sequence Database: major new developments  

Microsoft Academic Search

The EMBL Nucleotide Sequence Database (http:\\/\\/ www.ebi.ac.uk\\/embl\\/) incorporates, organizes and distributes nucleotide sequences from all available public sources. The database is located and main- tained at the European Bioinformatics Institute (EBI) near Cambridge, UK. In an international collabora- tion with DDBJ (Japan) and GenBank (USA), data are exchanged amongst the collaborating databases on a daily basis to achieve optimal synchronization.

Guenter Stoesser; Wendy Baker; Alexandra Van Den Broek; Maria Garcia-pastor; Carola Kanz; Tamara Kulikova; Rasko Leinonen; Quan Lin; Vincent Lombard; Rodrigo Lopez; Renato Mancuso; Francesco Nardone; Peter Stoehr; Mary Ann Tuli; Katerina Tzouvara; Robert Vaughan

2003-01-01

383

The HITRAN 2008 Molecular Spectroscopic Database  

NASA Technical Reports Server (NTRS)

This paper describes the status of the 2008 edition of the HITRAN molecular spectroscopic database. The new edition is the first official public release since the 2004 edition, although a number of crucial updates had been made available online since 2004. The HITRAN compilation consists of several components that serve as input for radiative-transfer calculation codes: individual line parameters for the microwave through visible spectra of molecules in the gas phase; absorption cross-sections for molecules having dense spectral features, i.e., spectra in which the individual lines are not resolved; individual line parameters and absorption cross sections for bands in the ultra-violet; refractive indices of aerosols, tables and files of general properties associated with the database; and database management software. The line-by-line portion of the database contains spectroscopic parameters for forty-two molecules including many of their isotopologues.

Rothman, Laurence S.; Gordon, Iouli E.; Barbe, Alain; Benner, D. Chris; Bernath, Peter F.; Birk, Manfred; Boudon, V.; Brown, Linda R.; Campargue, Alain; Champion, J.-P.; Chance, Kelly V.; Coudert, L. H.; Sung, K.; Toth, R. A.

2009-01-01

384

Plant databases and data analysis tools  

Technology Transfer Automated Retrieval System (TEKTRAN)

It is anticipated that the coming years will see the generation of large datasets including diagnostic markers in several plant species with emphasis on crop plants. To use these datasets effectively in any plant breeding program, it is essential to have the information available via public database...

385

The Drinking Water Treatability Database (Poster)  

EPA Science Inventory

Drinking Water Treatability Database (TDB) will provide data taken from the literature on the control of contaminants in drinking water, and will be housed on an interactive, publicly-available USEPA web site. It can be used for identifying effective treatment processes, recogni...

386

National Game Management Database of Hungary  

Microsoft Academic Search

Advances in ecological science and increasing public environmental awareness have resulted in changes in the management of renewable natural resources. To achieve sustainable use of wildlife, managers need reliable data on populations, habitats, and the complexities of ecological interactions. The National Game Management Database (NGMD) was first mandated by the Hungarian Game Management and Hunting Law in 1996. In this

Sándor Csányi; Krisztina Sonkoly

2010-01-01

387

A Database System for Course Administration.  

ERIC Educational Resources Information Center

Describes a computer-assisted testing system which produces multiple-choice examinations for a college course in business administration. The system uses SPIRES (Stanford Public Information REtrieval System) to manage a database of questions and related data, mark-sense cards for machine grading tests, and ACL (6) (Audit Command Language) to…

Benbasat, Izak; And Others

1982-01-01

388

THE DRINKING WATER TREATABILITY DATABASE (Slides)  

EPA Science Inventory

The Drinking Water Treatability Database (TDB) assembles referenced data on the control of contaminants in drinking water, housed on an interactive, publicly-available, USEPA web site (www.epa.gov/tdb). The TDB is of use to drinking water utilities, treatment process design engin...

389

THE DRINKING WATER TREATABILITY DATABASE (Conference Paper)  

EPA Science Inventory

The Drinking Water Treatability Database (TDB) assembles referenced data on the control of contaminants in drinking water, housed on an interactive, publicly-available, USEPA web site (www.epa.gov/tdb). The TDB is of use to drinking water utilities, treatment process design engin...

390

The HITRAN 2008 molecular spectroscopic database  

Microsoft Academic Search

This paper describes the status of the 2008 edition of the HITRAN molecular spectroscopic database. The new edition is the first official public release since the 2004 edition, although a number of crucial updates had been made available online since 2004. The HITRAN compilation consists of several components that serve as input for radiative-transfer calculation codes: individual line parameters for

L. S. Rothman; I. E. Gordon; A. Barbe; D. Chris Benner; P. F. Bernath; M. Birk; V. Boudon; L. R. Brown; A. Campargue; J.-P. Champion; K. Chance; L. H. Coudert; V. Dana; V. M. Devi; S. Fally; J.-M. Flaud; R. R. Gamache; A. Goldman; D. Jacquemart; I. Kleiner; N. Lacome; W. J. Lafferty; J.-Y. Mandin; S. T. Massie; S. N. Mikhailenko; C. E. Miller; N. Moazzen-Ahmadi; O. V. Naumenko; A. V. Nikitin; J. Orphal; V. I. Perevalov; A. Perrin; A. Predoi-Cross; C. P. Rinsland; M. Rotger; M. Šime?ková; M. A. H. Smith; K. Sung; S. A. Tashkun; J. Tennyson; R. A. Toth; A. C. Vandaele; J. Vander Auwera

2009-01-01

391

DNA Profiling of Convicted Offender Samples for the Combined DNA Index System  

ERIC Educational Resources Information Center

The cornerstone of forensic chemistry is that a perpetrator inevitably leaves trace evidence at a crime scene. One important type of evidence is DNA, which has been instrumental in both the implication and exoneration of thousands of suspects in a wide range of crimes. The Combined DNA Index System (CODIS), a network of DNA databases, provides…

Millard, Julie T

2011-01-01

392

48 CFR 504.602-71 - Federal Procurement Data System-Public access to data.  

Code of Federal Regulations, 2010 CFR

...System—Public access to data. (a) The FPDS database . The General Services Administration awarded...operation of the Federal Procurement Data System (FPDS) database. That database includes information reported by departments...

2010-10-01

393

48 CFR 504.602-71 - Federal Procurement Data System-Public access to data.  

Code of Federal Regulations, 2011 CFR

...System—Public access to data. (a) The FPDS database . The General Services Administration awarded...operation of the Federal Procurement Data System (FPDS) database. That database includes information reported by departments...

2011-10-01

394

A catalog of new eclipsing binaries in the Kepler database  

E-print Network

In this thesis, we present a catalog of binary stars discovered in the publicly available Kepler database, none of which were included in previous such catalogs published by the Kepler science team. A brief review of other ...

Kotson, Michael Christopher

2012-01-01

395

Publicity and public relations  

NASA Technical Reports Server (NTRS)

This paper addresses approaches to using publicity and public relations to meet the goals of the NASA Space Grant College. Methods universities and colleges can use to publicize space activities are presented.

Fosha, Charles E.

1990-01-01

396

The problems and promise of DNA barcodes for species diagnosis of primate biomaterials  

PubMed Central

The Integrated Primate Biomaterials and Information Resource (www.IPBIR.org) provides essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing DNA and RNA derived from primate cell cultures. The IPBIR uses mitochondrial cytochrome c oxidase subunit I sequences to verify the identity of samples for quality control purposes in the accession, cell culture, DNA extraction processes and prior to shipping to end users. As a result, IPBIR is accumulating a database of ‘DNA barcodes’ for many species of primates. However, this quality control process is complicated by taxon specific patterns of ‘universal primer’ failure, as well as the amplification or co-amplification of nuclear pseudogenes of mitochondrial origins. To overcome these difficulties, taxon specific primers have been developed, and reverse transcriptase PCR is utilized to exclude these extraneous sequences from amplification. DNA barcoding of primates has applications to conservation and law enforcement. Depositing barcode sequences in a public database, along with primer sequences, trace files and associated quality scores, makes this species identification technique widely accessible. Reference DNA barcode sequences should be derived from, and linked to, specimens of known provenance in web-accessible collections in order to validate this system of molecular diagnostics. PMID:16214744

Lorenz, Joseph G; Jackson, Whitney E; Beck, Jeanne C; Hanner, Robert

2005-01-01

397

The Vocational Guidance Research Database: A Scientometric Approach  

ERIC Educational Resources Information Center

The scientometric study of scientific output through publications in specialized journals cannot be undertaken exclusively with the databases available today. For this reason, the objective of this article is to introduce the "Base de Datos de Investigacion en Orientacion Vocacional" [Vocational Guidance Research Database], based on the use of…

Flores-Buils, Raquel; Gil-Beltran, Jose Manuel; Caballer-Miedes, Antonio; Martinez-Martinez, Miguel Angel

2012-01-01

398

Database for Earthquake Strong Motion Studies in Italy  

Microsoft Academic Search

We describe an Italian database of strong ground motion recordings and databanks delineating conditions at the instrument sites and characteristics of the seismic sources. The strong motion database consists of 247 corrected recordings from 89 earthquakes and 101 recording stations. Uncorrected recordings were drawn from public web sites and processed on a record-by-record basis using a procedure utilized in the

Giuseppe Scasserra; Jonathan P. Stewart; Robert E. Kayen; Giuseppe Lanzo

2009-01-01

399

Database User Aids and Materials--A Study.  

ERIC Educational Resources Information Center

Based on information solicited from database producers which had files publicly available on SDC and/or Lockheed, this study is intended to help searchers assess available database support materials with regard to their cost, format, depth, and purpose. The eight assumptions addressed cover the following areas: (1) the amount of reference material…

Unruh, Betty

400

A web-database of mammalian morphology and a reanalysis of placental phylogeny  

PubMed Central

Background Recent publications concerning the interordinal phylogeny of placental mammals have converged on a common signal, consisting of four major radiations with some ambiguity regarding the placental root. The DNA data with which these relationships have been reconstructed are easily accessible from public databases; access to morphological characters is much more difficult. Here, I present a graphical web-database of morphological characters focusing on placental mammals, in tandem with a combined-data phylogenetic analysis of placental mammal phylogeny. Results The results reinforce the growing consensus regarding the extant placental mammal clades of Afrotheria, Xenarthra, Euarchontoglires, and Laurasiatheria. Unweighted parsimony applied to all DNA sequences and insertion-deletion (indel) characters of extant taxa alone support a placental root at murid rodents; combined with morphology this shifts to Afrotheria. Bayesian analyses of morphology, indels, and DNA support both a basal position for Afrotheria and the position of Cretaceous eutherians outside of crown Placentalia. Depending on treatment of third codon positions, the affinity of several fossils (Leptictis,Paleoparadoxia, Plesiorycteropus and Zalambdalestes) vary, highlighting the potential effect of sequence data on fossils for which such data are missing. Conclusion The combined dataset supports the location of the placental mammal root at Afrotheria or Xenarthra, not at Erinaceus or rodents. Even a small morphological dataset can have a marked influence on the location of the root in a combined-data analysis. Additional morphological data are desirable to better reconstruct the position of several fossil taxa; and the graphic-rich, web-based morphology data matrix presented here will make it easier to incorporate more taxa into a larger data matrix. PMID:17608930

Asher, Robert J

2007-01-01

401

HMDB: the Human Metabolome Database.  

PubMed

The Human Metabolome Database (HMDB) is currently the most complete and comprehensive curated collection of human metabolite and human metabolism data in the world. It contains records for more than 2180 endogenous metabolites with information gathered from thousands of books, journal articles and electronic databases. In addition to its comprehensive literature-derived data, the HMDB also contains an extensive collection of experimental metabolite concentration data compiled from hundreds of mass spectra (MS) and Nuclear Magnetic resonance (NMR) metabolomic analyses performed on urine, blood and cerebrospinal fluid samples. This is further supplemented with thousands of NMR and MS spectra collected on purified, reference metabolites. Each metabolite entry in the HMDB contains an average of 90 separate data fields including a comprehensive compound description, names and synonyms, structural information, physico-chemical data, reference NMR and MS spectra, biofluid concentrations, disease associations, pathway information, enzyme data, gene sequence data, SNP and mutation data as well as extensive links to images, references and other public databases. Extensive searching, relational querying and data browsing tools are also provided. The HMDB is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. The HMDB is available at: www.hmdb.ca. PMID:17202168

Wishart, David S; Tzur, Dan; Knox, Craig; Eisner, Roman; Guo, An Chi; Young, Nelson; Cheng, Dean; Jewell, Kevin; Arndt, David; Sawhney, Summit; Fung, Chris; Nikolai, Lisa; Lewis, Mike; Coutouly, Marie-Aude; Forsythe, Ian; Tang, Peter; Shrivastava, Savita; Jeroncic, Kevin; Stothard, Paul; Amegbey, Godwin; Block, David; Hau, David D; Wagner, James; Miniaci, Jessica; Clements, Melisa; Gebremedhin, Mulu; Guo, Natalie; Zhang, Ying; Duggan, Gavin E; Macinnis, Glen D; Weljie, Alim M; Dowlatabadi, Reza; Bamforth, Fiona; Clive, Derrick; Greiner, Russ; Li, Liang; Marrie, Tom; Sykes, Brian D; Vogel, Hans J; Querengesser, Lori

2007-01-01

402

Federal Register document image database  

NASA Astrophysics Data System (ADS)

A new, fully-automated process has been developed at NIST to derive ground truth for document images. The method involves matching optical character recognition (OCR) results from a page with typesetting files for an entire book. Public domain software used to derive the ground truth is provided in the form of Perl scripts and C source code, and includes new, more efficient string alignment technology and a word- level scoring package. With this ground truthing technology, it is now feasible to produce much larger data sets, at much lower cost, than was ever possible with previous labor- intensive, manual data collection projects. Using this method, NIST has produced a new document image database for evaluating Document Analysis and Recognition technologies and Information Retrieval systems. The database produced contains scanned images, SGML-tagged ground truth text, commercial OCR results, and image quality assessment results for pages published in the 1994 Federal Register. These data files are useful in a wide variety of experiments and research. There were roughly 250 issues, comprised of nearly 69,000 pages, published in the Federal Register in 1994. This volume of the database contains the pages of 20 books published in January of that year. In all, there are 4711 page images provided, with 4519 of them having corresponding ground truth. This volume is distributed on two ISO-9660 CD- ROMs. Future volumes may be released, depending on the level of interest.

Garris, Michael D.; Janet, Stanley A.; Klein, William W.

1999-01-01

403

International Regulation Database  

NSDL National Science Digital Library

Created and maintained by the Organisation for Economic Co-operation and Development (OECD), the International Regulation Database is a "comprehensive internationally-comparable set of information about the state of regulation and market structures in OECD countries." The contents of the database are derived primarily from an ad hoc questionnaire that was given to OECD member countries in 1998. The database contains over 1,100 variables for each country and includes both broad regulations dealing with product markets, such as "state control of business enterprises" and international trade and investment barriers, as well as sector-specific regulations for areas such as telecommunications, retail distribution, and electricity supply. The database must be downloaded to users's computers, and is offered in both Access and Excel versions. An eleven-page, detailed description of the database's contents, structure, and use is also available, as is a Users' Guide, which offers step-by-step instructions for manipulating the Access database.

404

Electricity Database Files  

NSDL National Science Digital Library

The Electricity Database Files Web site from the Department of Energy's Energy Information Administration division contains several helpful resources. The site's two main categories are entitled Electric Generator Databases and Power Plant Databases, which contain more than a dozen links to related information. These include everything from an Annual Electric Generator Report, Electric Utilities Database, and a Wholesale Electric Trade Database, to a Clean Air Act Database Browser that provides information about electricity generators that must comply with the sulfur dioxide provisions of the Clean Air Act Amendments of 1990. This unique and informative collection, besides being easy to access, makes utilizing the information simple by allowing users to download the files as either Microsoft Access or Excel files.

405

2010 Worldwide Gasification Database  

DOE Data Explorer

The 2010 Worldwide Gasification Database describes the current world gasification industry and identifies near-term planned capacity additions. The database lists gasification projects and includes information (e.g., plant location, number and type of gasifiers, syngas capacity, feedstock, and products). The database reveals that the worldwide gasification capacity has continued to grow for the past several decades and is now at 70,817 megawatts thermal (MWth) of syngas output at 144 operating plants with a total of 412 gasifiers.

406

Databases and automated reasoning  

SciTech Connect

The design of application systems incorporating automated reasoning technology requires an understanding of database design, familiarity with various types of automated reasoning methods, and an integrated view of the database and reasoning system. We describe here the relationship, based on the common language of first-order logic, between entity-relationship database design techniques and automated reasoning systems. We include a brief overview of logic programming, automated theorem proving, and production-rule systems as separate but related branches of automated reasoning.

Lusk, E.L.; Overbeek, R.A.

1985-01-01

407

Trends in Database Research  

Microsoft Academic Search

Research in databases has played a vital role in developing information system technology and also the outcome of this research\\u000a has been very successful resulting in great potential for industry. The database industry is generating billions of dollars\\u000a of business annually. It has estimated that the database industry itself has generated $42 billion revenue in 2000 and this\\u000a market is

Mukesh K. Mohania; Yahiko Kambayashi; A. Min Tjoa; Roland Wagner; Ladjel Bellatreche

2001-01-01

408

USCM Mayoral Elections Database  

NSDL National Science Digital Library

The US Conference of Mayors (USCM) (see the January 1, 1999 Scout Report) provides the Mayoral Elections Database. The database allows citizens from all 50 states and the District of Columbia to locate information on mayoral elections held in 1999. Users may search the database by city, state, political party, or name of candidate. Searches yield city name, state, party and name of election winner, percentage of votes earned by winner, and month of election. [AO

409

DNA microarray (spot) .  

E-print Network

1. DNA microarray DNA (spot) . DNA probe , probe (hybridization) . DNA microarray cDNA oligonucleotide oligonucleotide cDNA probe . oligonucleotide microarray , DNA , probe . oligonucleotide microarray probe

410

The Martian Climate Database  

NSDL National Science Digital Library

This site features access to a database of statistics that was developed in order to describe the climate and surface environment of Mars. The database provides a valuable resource for scientific studies of the Martian atmosphere. The database is based directly on output from multi-annual integrations of two General Circulation Models (GCMs) which were developed jointly at Laboratoire de Météorologie Dynamique du CNRS, Paris, and the University of Oxford, with support from the European Space Agency. The site also includes an online version of a poster that gives examples of database output, including comparisons with previous observations.

S.R. Lewis

411

Databases for LDEF results  

NASA Technical Reports Server (NTRS)

One of the objectives of the team supporting the LDEF Systems and Materials Special Investigative Groups is to develop databases of experimental findings. These databases identify the hardware flown, summarize results and conclusions, and provide a system for acknowledging investigators, tracing sources of data, and future design suggestions. To date, databases covering the optical experiments, and thermal control materials (chromic acid anodized aluminum, silverized Teflon blankets, and paints) have been developed at Boeing. We used the Filemaker Pro software, the database manager for the Macintosh computer produced by the Claris Corporation. It is a flat, text-retrievable database that provides access to the data via an intuitive user interface, without tedious programming. Though this software is available only for the Macintosh computer at this time, copies of the databases can be saved to a format that is readable on a personal computer as well. Further, the data can be exported to more powerful relational databases, capabilities, and use of the LDEF databases and describe how to get copies of the database for your own research.

Bohnhoff-Hlavacek, Gail

1992-01-01

412

CDD: NCBI's conserved domain database.  

PubMed

NCBI's CDD, the Conserved Domain Database, enters its 15(th) year as a public resource for the annotation of proteins with the location of conserved domain footprints. Going forward, we strive to improve the coverage and consistency of domain annotation provided by CDD. We maintain a live search system as well as an archive of pre-computed domain annotation for sequences tracked in NCBI's Entrez protein database, which can be retrieved for single sequences or in bulk. We also maintain import procedures so that CDD contains domain models and domain definitions provided by several collections available in the public domain, as well as those produced by an in-house curation effort. The curation effort aims at increasing coverage and providing finer-grained classifications of common protein domains, for which a wealth of functional and structural data has become available. CDD curation generates alignment models of representative sequence fragments, which are in agreement with domain boundaries as observed in protein 3D structure, and which model the structurally conserved cores of domain families as well as annotate conserved features. CDD can be accessed at http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml. PMID:25414356

Marchler-Bauer, Aron; Derbyshire, Myra K; Gonzales, Noreen R; Lu, Shennan; Chitsaz, Farideh; Geer, Lewis Y; Geer, Renata C; He, Jane; Gwadz, Marc; Hurwitz, David I; Lanczycki, Christopher J; Lu, Fu; Marchler, Gabriele H; Song, James S; Thanki, Narmada; Wang, Zhouxi; Yamashita, Roxanne A; Zhang, Dachuan; Zheng, Chanjuan; Bryant, Stephen H

2015-01-28

413

The PROSITE database, its status in 2002  

Microsoft Academic Search

PROSITE (Bairoch and Bucher (1994) Nucleic Acids Res., 22, 3583-3589; Hofmann et al. (1999) Nucleic Acids Res., 27, 215-219) is a method of identifying the functions of uncharacterized proteins translated from genomic or cDNA sequences. The PROSITE database (http:\\/\\/www.expasy.org\\/prosite\\/) consists of biologically significant patterns and profiles designed in such a way that with appropriate compu- tational tools it can rapidly

Laurent Falquet; Marco Pagni; Philipp Bucher; Nicolas Hulo; Christian J. A. Sigrist; Kay Hofmann; Amos Bairoch

2002-01-01

414

Southeast Asian diversity: first insights into the complex mtDNA structure of Laos  

PubMed Central

Background Vast migrations and subsequent assimilation processes have shaped the genetic composition of Southeast Asia, an area of close contact between several major ethnic groups. To better characterize the genetic variation of this region, we analyzed the entire mtDNA control region of 214 unrelated donors from Laos according to highest forensic quality standards. To detail the phylogeny, we inspected selected SNPs from the mtDNA coding region. For a posteriori data quality control, quasi-median network constructions and autosomal STR typing were performed. In order to describe the mtDNA setup of Laos more thoroughly, the data were subjected to population genetic comparisons with 16 East Asian groups. Results The Laos sample exhibited ample mtDNA diversity, reflecting the huge number of ethnic groups listed. We found several new, so far undescribed mtDNA lineages in this dataset and surrounding populations. The Laos population was characteristic in terms of haplotype composition and genetic structure, however, genetic comparisons with other Southeast Asian populations revealed limited, but significant genetic differentiation. Notable differences in the maternal relationship to the major indigenous Southeast Asian ethnolinguistic groups were detected. Conclusions In this study, we portray the great mtDNA variety of Laos for the first time. Our findings will contribute to clarify the migration history of the region. They encourage setting up regional and subpopulation databases, especially for forensic applications. The Laotian sequences will be incorporated into the collaborative EMPOP mtDNA database http://www.empop.org upon publication and will be available as the first mtDNA reference data for this country. PMID:21333001

2011-01-01

415

Report into a discordant result at D16S539 between SGM Plus® and PowerPlex® ESI 16 kits in a criminal case sample and implications for the UK National DNA Database upgrade.  

PubMed

Upon re-testing of a DNA extract as part of a defence examination, a discordant result was observed at D16S539. Further STR testing and DNA sequencing of the sample identified the cause as a primer binding site mutation which was shown to be a previously unreported SNP. The testing results obtained in this case are considered in light of the current ongoing Multiplex Upgrade Project in the UK and the likely increase in discordant results that may be observed once different next generation kits are introduced. PMID:24438784

Revoir, A; Ballard, D J; Syndercombe Court, D

2014-01-01

416

Central Asia Active Fault Database  

NASA Astrophysics Data System (ADS)

The ongoing collision of the Indian subcontinent with Asia controls active tectonics and seismicity in Central Asia. This motion is accommodated by faults that have historically caused devastating earthquakes and continue to pose serious threats to the population at risk. Despite international and regional efforts to assess seismic hazards in Central Asia, little attention has been given to development of a comprehensive database for active faults in the region. To address this issue and to better understand the distribution and level of seismic hazard in Central Asia, we are developing a publically available database for active faults of Central Asia (including but not limited to Afghanistan, Tajikistan, Kyrgyzstan, northern Pakistan and western China) using ArcGIS. The database is designed to allow users to store, map and query important fault parameters such as fault location, displacement history, rate of movement, and other data relevant to seismic hazard studies including fault trench locations, geochronology constraints, and seismic studies. Data sources integrated into the database include previously published maps and scientific investigations as well as strain rate measurements and historic and recent seismicity. In addition, high resolution Quickbird, Spot, and Aster imagery are used for selected features to locate and measure offset of landforms associated with Quaternary faulting. These features are individually digitized and linked to attribute tables that provide a description for each feature. Preliminary observations include inconsistent and sometimes inaccurate information for faults documented in different studies. For example, the Darvaz-Karakul fault which roughly defines the western margin of the Pamir, has been mapped with differences in location of up to 12 kilometers. The sense of motion for this fault ranges from unknown to thrust and strike-slip in three different studies despite documented left-lateral displacements of Holocene and late Pleistocene landforms observed near the fault trace.

Mohadjer, Solmaz; Ehlers, Todd A.; Kakar, Najibullah

2014-05-01

417

The RECONS 25 Parsec Database  

NASA Astrophysics Data System (ADS)

The REsearch Consortium On Nearby Stars (RECONS, www.recons.org) Team has been mapping the solar neighborhood since 1994. Nearby stars provide the fundamental framework upon which all of stellar astronomy is based, both for individual stars and stellar populations. The nearest stars are also the primary targets for extrasolar planet searches, and will undoubtedly play key roles in understanding the prevalence and structure of solar systems, and ultimately, in our search for life elsewhere.We have built the RECONS 25 Parsec Database to encourage and enable exploration of the Sun's nearest neighbors. The Database, slated for public release in 2015, contains 3088 stars, brown dwarfs, andexoplanets in 2184 systems as of October 1, 2014. All of these systems have accurate trigonometric parallaxes in the refereed literature placing them closer than 25.0 parsecs, i.e., parallaxes greater than 40 mas with errors less than 10 mas. Carefully vetted astrometric, photometric, and spectroscopic data are incorporated intothe Database from reliable sources, including significant original data collected by members of the RECONS Team.Current exploration of the solar neighborhood by RECONS, enabled by the Database, focuses on the ubiquitous red dwarfs, including: assessing the stellar companion population of ~1200 red dwarfs (Winters), investigating the astrophysical causes that spread red dwarfs of similar temperatures by a factor of 16 in luminosity (Pewett), and canvassing ~3000 red dwarfs for excess emission due to unseen companions and dust (Silverstein). In addition, a decade long astrometric survey of ~500 red dwarfs in the southern sky has begun, in an effort to understand the stellar, brown dwarf, and planetary companion populations for the stars that make up at least 75% of all stars in the Universe.This effort has been supported by the NSF through grants AST-0908402, AST-1109445, and AST-1412026, and via observations made possible by the SMARTS Consortium.

Henry, Todd J.; Jao, Wei-Chun; Pewett, Tiffany; Riedel, Adric R.; Silverstein, Michele L.; Slatten, Kenneth J.; Winters, Jennifer G.; Recons Team

2015-01-01

418

wDBTF: an integrated database resource for studying wheat transcription factor families  

PubMed Central

Background Transcription factors (TFs) regulate gene expression by interacting with promoters of their target genes and are classified into families based on their DNA-binding domains. Genes coding for TFs have been identified in the sequences of model plant genomes. The rice (Oryza sativa spp. japonica) genome contains 2,384 TF gene models, which represent the mRNA transcript of a locus, classed into 63 families. Results We have created an extensive list of wheat (Triticum aestivum L) TF sequences based on sequence homology with rice TFs identified and classified in the Database of Rice Transcription Factors (DRTF). We have identified 7,112 wheat sequences (contigs and singletons) from a dataset of 1,033,960 expressed sequence tag and mRNA (ET) sequences available. This number is about three times the number of TFs in rice so proportionally is very similar if allowance is made for the hexaploidy of wheat. Of these sequences 3,820 encode gene products with a DNA-binding domain and thus were confirmed as potential regulators. These 3,820 sequences were classified into 40 families and 84 subfamilies and some members defined orphan families. The results were compiled in the Database of Wheat Transcription Factor (wDBTF), an inventory available on the web http://wwwappli.nantes.inra.fr:8180/wDBFT/. For each accession, a link to its library source and its Affymetrix identification number is provided. The positions of Pfam (protein family database) motifs were given when known. Conclusions wDBTF collates 3,820 wheat TF sequences validated by the presence of a DNA-binding domain out of 7,112 potential TF sequences identified from publicly available gene expression data. We also incorporated in silico expression data on these TFs into the database. Thus this database provides a major resource for systematic studies of TF families and their expression in wheat as illustrated here in a study of DOF family members expressed during seed development. PMID:20298594

2010-01-01

419

Toward unification of taxonomy databases in a distributed computer environment  

SciTech Connect

All the taxonomy databases constructed with the DNA databases of the international DNA data banks are powerful electronic dictionaries which aid in biological research by computer. The taxonomy databases are, however not consistently unified with a relational format. If we can achieve consistent unification of the taxonomy databases, it will be useful in comparing many research results, and investigating future research directions from existent research results. In particular, it will be useful in comparing relationships between phylogenetic trees inferred from molecular data and those constructed from morphological data. The goal of the present study is to unify the existent taxonomy databases and eliminate inconsistencies (errors) that are present in them. Inconsistencies occur particularly in the restructuring of the existent taxonomy databases, since classification rules for constructing the taxonomy have rapidly changed with biological advancements. A repair system is needed to remove inconsistencies in each data bank and mismatches among data banks. This paper describes a new methodology for removing both inconsistencies and mismatches from the databases on a distributed computer environment. The methodology is implemented in a relational database management system, SYBASE.

Kitakami, Hajime [Hiroshima City Univ. (Japan); Tateno, Yoshio; Gojobori, Takashi [National Institute of Genetics, Shizuoka-Ken (Japan)

1994-12-31

420

Physical database design for relational databases  

Microsoft Academic Search

This paper describes the concepts used in the implementation of DBDSGN, an experimental physical design tool for relational databases developed at the IBM San Jose Research Laboratory. Given a workload for System R (consisting of a set of SQL statements and their execution frequencies), DBDSGN suggests physical configurations for efficient performance. Each configuration consists of a set of indices and

Sheldon J. Finkelstein; Mario Schkolnick; Paolo Tiberio

1988-01-01

421

A Quality System Database  

NASA Technical Reports Server (NTRS)

A quality system database (QSD), and software to administer the database, were developed to support recording of administrative nonconformance activities that involve requirements for documentation of corrective and/or preventive actions, which can include ISO 9000 internal quality audits and customer complaints.

Snell, William H.; Turner, Anne M.; Gifford, Luther; Stites, William

2010-01-01

422

Pharmacoepidemiology and Healthcare Databases  

Cancer.gov

These databases can be used to access national and international data that can help answer some of the outstanding questions of cancer-related outcomes (positive or negative) associated with pharmaceuticals. Some of the databases are linked to a table of pharmacoepidemiology data elements, which provides a snapshot of the material contained therein.

423

ETD - Exoplanet Transit Database  

NASA Astrophysics Data System (ADS)

Introduction of Exoplanet Transit Database (ETD), an internet portal, which offers all necessary informations for exoplanet transit observation. Scheduling, list of previously obtained data and on-line algorithm for photometric data processing, which determines the mid-transit time, duration and depth of a transit The Exoplanet Transit Database can be found at http://var.astro.cz/etd.

Brát, L.; Poddaný, S.; Pejcha, O.; Zejda, M.

2010-12-01

424

World Database of Crystallographers  

NSDL National Science Digital Library

The World Database of Crystallographers and of Other Scientists Employing Crystallographic Methods is offered by the International Union of Crystallography. The simple database can be searched by family name, title, interests, address, and various other criteria. Results include basic information such as full name, position, institution address, degrees held, key interests, and contact information. Those seeking such specific information will appreciate this unique resource.

425

Database-backed websites  

Microsoft Academic Search

This paper describes a set of labs packaged as a tutorial and designed to teach students how to build database-backed web sites. These labs can be used within a variety of existing courses and need only three weeks to complete. Students need prerequisite knowledge of HTML, Visual Basic or VBScript, and the ability to build a simple database using Microsoft

Jean Mehta

2002-01-01

426

Steam Properties Database  

National Institute of Standards and Technology Data Gateway

SRD 10 NIST/ASME Steam Properties Database (PC database for purchase)   Based upon the International Association for the Properties of Water and Steam (IAPWS) 1995 formulation for the thermodynamic properties of water and the most recent IAPWS formulations for transport and other properties, this updated version provides water properties over a wide range of conditions according to the accepted international standards.

427

Clinician use of a pediatric cardiology database on a microcomputer.  

PubMed

A pediatric cardiology database was designed and implemented on a microcomputer using the MEDUS/A (Harvard School of Public Health) database management system. This database has potential utility in the areas of clinical research, patient management, and administration. Initial uses of the system include a study of ventricular septal defects, and automation of pacemaker clinic and cardiac catheterization laboratory records. Clinicians with little or no programming experience can alter the database structure and tailor complicated applications to their particular needs. Preliminary evaluation of the system is presented. PMID:3841043

Soffer, L J; Wolfenson, L B; Sivakoff, M C

1985-12-01

428

16 CFR 1102.30 - Publication of manufacturer comments.  

Code of Federal Regulations, 2011 CFR

...REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE (Eff. Jan. 10, 2011) Procedural Requirements § 1102...1102.24, and 1102.26, the Commission will publish in the Database manufacturer comments submitted in response to a report of...

2011-01-01

429

Cascadia Tsunami Deposit Database  

USGS Publications Warehouse

The Cascadia Tsunami Deposit Database contains data on the location and sedimentological properties of tsunami deposits found along the Cascadia margin. Data have been compiled from 52 studies, documenting 59 sites from northern California to Vancouver Island, British Columbia that contain known or potential tsunami deposits. Bibliographical references are provided for all sites included in the database. Cascadia tsunami deposits are usually seen as anomalous sand layers in coastal marsh or lake sediments. The studies cited in the database use numerous criteria based on sedimentary characteristics to distinguish tsunami deposits from sand layers deposited by other processes, such as river flooding and storm surges. Several studies cited in the database contain evidence for more than one tsunami at a site. Data categories include age, thickness, layering, grainsize, and other sedimentological characteristics of Cascadia tsunami deposits. The database documents the variability observed in tsunami deposits found along the Cascadia margin.

Peters, Robert; Jaffe, Bruce; Gelfenbaum, Guy; Peterson, Curt

2003-01-01

430

The Kidney Development Database.  

PubMed

The Kidney Development Database is a bioinformatics resource dedicated to providing easily accessible information on gene expression during the development of the pro-, meso-, and metanephroi of a range of vertebrates. It also contains data on mutant phenotypes and on the effects of experimental manipulation of kidneys developing in culture. The database is searchable by gene name or by expression pattern. It is now being used as a test bed for more "advanced" search strategies that measure hypotheses of gene interactions against expression data to test for any clashes that would make the hypotheses untenable and that scan the database for potentially interesting correlations between changes in gene expression. The Kidney Development Database can be accessed free of charge via the World Wide Web at either of the following uniform resource locators (URLs); http://golgi.ana.ed.ac.uk/kidhome.html, and http://www.ana.ed.ac.uk/anatomy/database/kidbase/ kidhome.html. PMID:10322627

Davies, J A

1999-01-01

431

Database Constraints Applied to Metabolic Pathway Reconstruction Tools  

PubMed Central

Our group developed two biological applications, Biblio-MetReS and Homol-MetReS, accessing the same database of organisms with annotated genes. Biblio-MetReS is a data-mining application that facilitates the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows functional (re)annotation of proteomes, to properly identify both the individual proteins involved in the process(es) of interest and their function. It also enables the sets of proteins involved in the process(es) in different organisms to be compared directly. The efficiency of these biological applications is directly related to the design of the shared database. We classified and analyzed the different kinds of access to the database. Based on this study, we tried to adjust and tune the configurable parameters of the database server to reach the best performance of the communication data link to/from the database system. Different database technologies were analyzed. We started the study with a public relational SQL database, MySQL. Then, the same database was implemented by a MapReduce-based database named HBase. The results indicated that the standard configuration of MySQL gives an acceptable performance for low or medium size databases. Nevertheless, tuning database parameters can greatly improve the performance and lead to very competitive runtimes. PMID:25202745

Vilaplana, Jordi; Solsona, Francesc; Teixido, Ivan; Usié, Anabel; Karathia, Hiren; Alves, Rui; Mateo, Jordi

2014-01-01

432

ORIGINAL PAPER STRs vs. SNPs: thoughts on the future of forensic DNA testing  

E-print Network

applications. Keywords DNA Á DNA typing Á DNA profiling Á Short tandem repeat Á Single nucleotide polymorphism) markers, has become the primary means for forensic DNA profiling over the past decade [1]. Large national DNA databases now exist containing millions of STR profiles based on a few core STR markers [2, 3

433

Pfam: the protein families database  

PubMed Central

Pfam, available via servers in the UK (http://pfam.sanger.ac.uk/) and the USA (http://pfam.janelia.org/), is a widely used database of protein families, containing 14 831 manually curated entries in the current release, version 27.0. Since the last update article 2 years ago, we have generated 1182 new families and maintained sequence coverage of the UniProt Knowledgebase (UniProtKB) at nearly 80%, despite a 50% increase in the size of the underlying sequence database. Since our 2012 article describing Pfam, we have also undertaken a comprehensive review of the features that are provided by Pfam over and above the basic family data. For each feature, we determined the relevance, computational burden, usage statistics and the functionality of the feature in a website context. As a consequence of this review, we have removed some features, enhanced others and developed new ones to meet the changing demands of computational biology. Here, we describe the changes to Pfam content. Notably, we now provide family alignments based on four different representative proteome sequence data sets and a new interactive DNA search interface. We also discuss the mapping between Pfam and known 3D structures. PMID:24288371

Finn, Robert D.; Bateman, Alex; Clements, Jody; Coggill, Penelope; Eberhardt, Ruth Y.; Eddy, Sean R.; Heger, Andreas; Hetherington, Kirstie; Holm, Liisa; Mistry, Jaina; Sonnhammer, Erik L. L.; Tate, John; Punta, Marco

2014-01-01

434

Pfam: the protein families database.  

PubMed

Pfam, available via servers in the UK (http://pfam.sanger.ac.uk/) and the USA (http://pfam.janelia.org/), is a widely used database of protein families, containing 14 831 manually curated entries in the current release, version 27.0. Since the last update article 2 years ago, we have generated 1182 new families and maintained sequence coverage of the UniProt Knowledgebase (UniProtKB) at nearly 80%, despite a 50% increase in the size of the underlying sequence database. Since our 2012 article describing Pfam, we have also undertaken a comprehensive review of the features that are provided by Pfam over and above the basic family data. For each feature, we determined the relevance, computational burden, usage statistics and the functionality of the feature in a website context. As a consequence of this review, we have removed some features, enhanced others and developed new ones to meet the changing demands of computational biology. Here, we describe the changes to Pfam content. Notably, we now provide family alignments based on four different representative proteome sequence data sets and a new interactive DNA search interface. We also discuss the mapping between Pfam and known 3D structures. PMID:24288371

Finn, Robert D; Bateman, Alex; Clements, Jody; Coggill, Penelope; Eberhardt, Ruth Y; Eddy, Sean R; Heger, Andreas; Hetherington, Kirstie; Holm, Liisa; Mistry, Jaina; Sonnhammer, Erik L L; Tate, John; Punta, Marco

2014-01-01

435

Proposal for a High Energy Nuclear Database  

E-print Network

We propose to develop a high-energy heavy-ion experimental database and make it accessible to the scientific community through an on-line interface. This database will be searchable and cross-indexed with relevant publications, including published detector descriptions. Since this database will be a community resource, it requires the high-energy nuclear physics community's financial and manpower support. This database should eventually contain all published data from Bevalac, AGS and SPS to RHIC and LHC energies, proton-proton to nucleus-nucleus collisions as well as other relevant systems, and all measured observables. Such a database would have tremendous scientific payoff as it makes systematic studies easier and allows simpler benchmarking of theoretical models to a broad range of old and new experiments. Furthermore, there is a growing need for compilations of high-energy nuclear data for applications including stockpile stewardship, technology development for inertial confinement fusion and target and source development for upcoming facilities such as the Next Linear Collider. To enhance the utility of this database, we propose periodically performing evaluations of the data and summarizing the results in topical reviews.

David A. Brown Ramona Vogt

2005-04-01

436

Proposal for a High Energy Nuclear Database  

SciTech Connect

We propose to develop a high-energy heavy-ion experimental database and make it accessible to the scientific community through an on-line interface. This database will be searchable and cross-indexed with relevant publications, including published detector descriptions. Since this database will be a community resource, it requires the high-energy nuclear physics community's financial and manpower support. This database should eventually contain all published data from Bevalac and AGS to RHIC to CERN-LHC energies, proton-proton to nucleus-nucleus collisions as well as other relevant systems, and all measured observables. Such a database would have tremendous scientific payoff as it makes systematic studies easier and allows simpler benchmarking of theoretical models to a broad range of old and new experiments. Furthermore, there is a growing need for compilations of high-energy nuclear data for applications including stockpile stewardship, technology development for inertial confinement fusion and target and source development for upcoming facilities such as the Next Linear Collider. To enhance the utility of this database, we propose periodically performing evaluations of the data and summarizing the results in topical reviews.

Brown, David A.; Vogt, Ramona

2005-03-31

437

Database of Mechanical Properties of Textile Composites  

NASA Technical Reports Server (NTRS)

This report describes the approach followed to develop a database for mechanical properties of textile composites. The data in this database is assembled from NASA Advanced Composites Technology (ACT) programs and from data in the public domain. This database meets the data documentation requirements of MIL-HDBK-17, Section 8.1.2, which describes in detail the type and amount of information needed to completely document composite material properties. The database focuses on mechanical properties of textile composite. Properties are available for a range of parameters such as direction, fiber architecture, materials, environmental condition, and failure mode. The composite materials in the database contain innovative textile architectures such as the braided, woven, and knitted materials evaluated under the NASA ACT programs. In summary, the database contains results for approximately 3500 coupon level tests, for ten different fiber/resin combinations, and seven different textile architectures. It also includes a limited amount of prepreg tape composites data from ACT programs where side-by-side comparisons were made.

Delbrey, Jerry

1996-01-01

438

Which specimens from a museum collection will yield DNA barcodes? A time series study of spiders in alcohol  

PubMed Central

Abstract We report initial results from an ongoing effort to build a library of DNA barcode sequences for Dutch spiders and investigate the utility of museum collections as a source of specimens for barcoding spiders. Source material for the library comes from a combination of specimens freshly collected in the field specifically for this project and museum specimens collected in the past. For the museum specimens, we focus on 31 species that have been frequently collected over the past several decades. A series of progressively older specimens representing these 31 species were selected for DNA barcoding. Based on the pattern of sequencing successes and failures, we find that smaller-bodied species expire before larger-bodied species as tissue sources for single-PCR standard DNA barcoding. Body size and age of oldest successful DNA barcode are significantly correlated after factoring out phylogenetic effects using independent contrasts analysis. We found some evidence that extracted DNA concentration is correlated with body size and inversely correlated with time since collection, but these relationships are neither strong nor consistent. DNA was extracted from all specimens using standard destructive techniques involving the removal and grinding of tissue. A subset of specimens was selected to evaluate nondestructive extraction. Nondestructive extractions significantly extended the DNA barcoding shelf life of museum specimens, especially small-bodied species, and yielded higher DNA concentrations compared to destructive extractions. All primary data are publically available through a Dryad archive and the Barcode of Life database. PMID:24453561

Miller, Jeremy A.; Beentjes, Kevin K.; van Helsdingen, Peter; IJland, Steven

2013-01-01

439

Numeric Databases in the Sciences.  

ERIC Educational Resources Information Center

Provides exploration into types of numeric databases available (also known as source databases, nonbibliographic databases, data-files, data-banks, fact banks); examines differences and similarities between bibliographic and numeric databases; identifies disciplines that utilize numeric databases; and surveys representative examples in the…

Meschel, S. V.

1984-01-01

440

The magnet components database system  

Microsoft Academic Search

The philosophy, structure, and usage MagCom, the SSC magnet components database, are described. The database has been implemented in Sybase (a powerful relational database management system) on a UNIX-based workstation at the Superconducting Super Collider Laboratory (SSCL); magnet project collaborators can access the database via network connections. The database was designed to contain the specifications and measured values of important

M. J. Baggett; R. Leedy; C. Saltmarsh; J. C. Tompkins

1990-01-01

441

NIST Standard Reference Database 17 NIST Chemical Kinetics Database  

E-print Network

NIST Standard Reference Database 17 __________________________________________________________ NIST Chemical Kinetics Database WindowsTM Version 2Q98 Users' Guide (NIST) uses its best efforts to deliver a high quality copy of the Database and to verify that the data

442

www.cleanenergysolutions.org INDIAN RENEWABLE ENERGY AND ENERGY EFFICIENCY POLICY DATABASE  

E-print Network

www.cleanenergysolutions.org INDIAN RENEWABLE ENERGY AND ENERGY EFFICIENCY POLICY DATABASE India) and India's Ministry of New and Renewable Energy (MNRE) have partnered to develop an online database programs. This public database, developed under the U.S.-India Energy Dialogue and the Clean Energy

443

A Study of the Impact of Statewide Database Licensing on Information Provision in Washington State  

Microsoft Academic Search

The Statewide Database Licensing (SDL) Project brought ProQuest, full-text periodicals and newspapers databases from Bell & Howell, to nearly every library in Washington State. The research presented here investigates the impact of statewide database licensing on the users of public, school and community college libraries. The study was conducted in two stages. At first, transaction log data from Bell &

Efthimis N. Efthimiadis; Harry Bruce

444

The Vera am Mittag German audio-visual emotional speech database  

Microsoft Academic Search

The lack of publicly available annotated databases is one of the major barriers to research advances on emotional informa- tion processing. In this contribution we present a recently col- lected database of spontaneous emotional speech in German which is being made available to the research community. The database consists of 12 hours of audio-visual recordings of the German TV talk

Michael Grimm; Kristian Kroschel; Shrikanth Narayanan

2008-01-01

445

Speechdat-e: five eastern european speech databases for voice-operated teleservices completed  

Microsoft Academic Search

In the Speechdat-E project five medium large telephonespeech databases have been collected for Czech, Hungarian,Polish, Russian, and Slovak. The project was recentlyconcluded. This paper reports briefly on the contents of thedatabases, elaborates on experiences gained from the datarecordings and from the validation of the databases. Theavailability of the databases to the public is addressed, too.

Henk van den Heuvel; Jérôme Boudy; Zsolt Bakcsi; Jan Cernocký; Valery Galunov; Julia Kochanina; Wojciech Majewski; Petr Pollák; Milan Rusko; Jerzy Sadowski; Piotr Staroniewicz; Herbert S. Tropf

2001-01-01

446

Release of ToxCastDB and ExpoCastDB databases  

EPA Science Inventory

EPA has released two databases - the Toxicity Forecaster database (ToxCastDB) and a database of chemical exposure studies (ExpoCastDB) - that scientists and the public can use to access chemical toxicity and exposure data. ToxCastDB users can search and download data from over 50...

447

National Environmental Publications Internet Site  

NSDL National Science Digital Library

National Environmental Publications Internet Site is maintained by the Environmental Protection Agency (EPA) and contains a database of over 9000 documents that have been published by the EPA. Searches can be attempted by keyword or by publication title, which should help make finding a particular document easy. Once found, the documents can be viewed, printed freely, or ordered directly from the EPA.

448

DoD: Database of Databases--updated molecular biology databases.  

PubMed

Database of Databases (DoD) is a collection of molecular biology databases extracted from Nucleic Acids Research, 2005 Database issue. DoD is constructed using javascript and html code. The 14 categories of 719 databases are provided with a search option, keyword help and database description linked to respective pages. Keyword help lists the search strings used to perform an individual search against categorized databases. Database description provides brief information about the database with a link to full-text article and main web page. DoD is available online and can be accessed at http://www.progenebio.in/DoD/DoD.htm. PMID:16610138

Babu, P Ajay; Boddepalli, Radha; Lakshmi, V Vasantha; Rao, G Nageswara

2005-01-01

449

Preparing the DNA for sequencing, Shane YeagerSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

Interviewee: Shane Yeager DNAi Location:Genome>The project>Players>Public Preparing the DNA for sequencing Shane Yeager, from the Whitehead Institute Center for Genome Research, explains the processes of storing and preparing DNA for sequencing.

2008-10-06

450

The NCBI Taxonomy database  

PubMed Central

The NCBI Taxonomy database (http://www.ncbi.nlm.nih.gov/taxonomy) is the standard nomenclature and classification repository for the International Nucleotide Sequence Database Collaboration (INSDC), comprising the GenBank, ENA (EMBL) and DDBJ databases. It includes organism names and taxonomic lineages for each of the sequences represented in the INSDC’s nucleotide and protein sequence databases. The taxonomy database is manually curated by a small group of scientists at the NCBI who use the current taxonomic literature to maintain a phylogenetic taxonomy for the source organisms represented in the sequence databases. The taxonomy database is a central organizing hub for many of the resources at the NCBI, and provides a means for clustering elements within other domains of NCBI web site, for internal linking between domains of the Entrez system and for linking out to taxon-specific external resources on the web. Our primary purpose is to index the domain of sequences as conveniently as possible for our user community. PMID:22139910

Federhen, Scott

2012-01-01

451

DNA Computing Hamiltonian path  

E-print Network

2014 DNA DNA #12;DNA Computing · Feynman · Adleman · DNASIMD · ... · · · · · DNADNA #12;DNA · DNA · · · · DNA · · #12;2000 2005 2010 1995 Hamiltonian path DNA tweezers DNA tile DNA origami DNA box Sierpinski DNA tile self assembly DNA logic gates Whiplash PCR DNA automaton DNA spider MAYA

Hagiya, Masami

452

Recent updates and developments to plant genome size databases  

PubMed Central

Two plant genome size databases have been recently updated and/or extended: the Plant DNA C-values database (http://data.kew.org/cvalues), and GSAD, the Genome Size in Asteraceae database (http://www.asteraceaegenomesize.com). While the first provides information on nuclear DNA contents across land plants and some algal groups, the second is focused on one of the largest and most economically important angiosperm families, Asteraceae. Genome size data have numerous applications: they can be used in comparative studies on genome evolution, or as a tool to appraise the cost of whole-genome sequencing programs. The growing interest in genome size and increasing rate of data accumulation has necessitated the continued update of these databases. Currently, the Plant DNA C-values database (Release 6.0, Dec. 2012) contains data for 8510 species, while GSAD has 1219 species (Release 2.0, June 2013), representing increases of 17 and 51%, respectively, in the number of species with genome size data, compared with previous releases. Here we provide overviews of the most recent releases of each database, and outline new features of GSAD. The latter include (i) a tool to visually compare genome size data between species, (ii) the option to export data and (iii) a webpage containing information about flow cytometry protocols. PMID:24288377

Garcia, Sònia; Leitch, Ilia J.; Anadon-Rosell, Alba; Canela, Miguel Á.; Gálvez, Francisco; Garnatje, Teresa; Gras, Airy; Hidalgo, Oriane; Johnston, Emmeline; Mas de Xaxars, Gemma; Pellicer, Jaume; Siljak-Yakovlev, Sonja; Vallès, Joan; Vitales, Daniel; Bennett, Michael D.

2014-01-01

453

Database for propagation models  

NASA Technical Reports Server (NTRS)

A propagation researcher or a systems engineer who intends to use the results of a propagation experiment is generally faced with various database tasks such as the selection of the computer software, the hardware, and the writing of the programs to pass the data through the models of interest. This task is repeated every time a new experiment is conducted or the same experiment is carried out at a different location generating different data. Thus the users of this data have to spend a considerable portion of their time learning how to implement the computer hardware and the software towards the desired end. This situation may be facilitated considerably if an easily accessible propagation database is created that has all the accepted (standardized) propagation phenomena models approved by the propagation research community. Also, the handling of data will become easier for the user. Such a database construction can only stimulate the growth of the propagation research it if is available to all the researchers, so that the results of the experiment conducted by one researcher can be examined independently by another, without different hardware and software being used. The database may be made flexible so that the researchers need not be confined only to the contents of the database. Another way in which the database may help the researchers is by the fact that they will not have to document the software and hardware tools used in their research since the propagation research community will know the database already. The following sections show a possible database construction, as well as properties of the database for the propagation research.

Kantak, Anil V.

1991-01-01

454

Use of administrative medical databases in population-based research.  

PubMed

Administrative medical databases are massive repositories of data collected in healthcare for various purposes. Such databases are maintained in hospitals, health maintenance organisations and health insurance organisations. Administrative databases may contain medical claims for reimbursement, records of health services, medical procedures, prescriptions, and diagnoses information. It is clear that such systems may provide a valuable variety of clinical and demographic information as well as an on-going process of data collection. In general, information gathering in these databases does not initially presume and is not planned for research purposes. Nonetheless, administrative databases may be used as a robust research tool. In this article, we address the subject of public health research that employs administrative data. We discuss the biases and the limitations of such research, as well as other important epidemiological and biostatistical key points specific to administrative database studies. PMID:24248997

Gavrielov-Yusim, Natalie; Friger, Michael

2014-03-01

455

Hybrid Terrain Database  

NASA Technical Reports Server (NTRS)

A prototype hybrid terrain database is being developed in conjunction with other databases and with hardware and software that constitute subsystems of aerospace cockpit display systems (known in the art as synthetic vision systems) that generate images to increase pilots' situation awareness and eliminate poor visibility as a cause of aviation accidents. The basic idea is to provide a clear view of the world around an aircraft by displaying computer-generated imagery derived from an onboard database of terrain, obstacle, and airport information.

Arthur, Trey

2006-01-01

456

NORTHWOODS Wildlife Habitat Database  

NSDL National Science Digital Library

Created through a joint effort of the USDA Forest Service's North Central Forest Experiment Station (NCFES) and seven national forests in the Upper Great Lakes Region, NORTHWOODS is a wildlife habitat database featuring "information about the habitat needs of 389 species of reptiles, amphibians, birds, and mammals in the Upper Great Lakes Region." The database compiles common and scientific names, species occurrences in 20 aquatic and terrestrial habitat types, species abundances and seasonal use in seven national forests, and species conservation status. The NORTHWOODS database is available in tab-delimited ASCII file format.

457

International Comparisions Database  

National Institute of Standards and Technology Data Gateway

International Comparisions Database (Web, free access)   The International Comparisons Database (ICDB) serves the U.S. and the Inter-American System of Metrology (SIM) with information based on Appendices B (International Comparisons), C (Calibration and Measurement Capabilities) and D (List of Participating Countries) of the Comit? International des Poids et Mesures (CIPM) Mutual Recognition Arrangement (MRA). The official source of the data is The BIPM key comparison database. The ICDB provides access to results of comparisons of measurements and standards organized by the consultative committees of the CIPM and the Regional Metrology Organizations.

458

The Mendel Database  

NSDL National Science Digital Library

The Mendel Database, part of the Mendel Plant Gene Nomenclature Database project by the Mendel Bioinformatics Group (UK), "aims to develop a common nomenclature for sequenced genes, based on gene families, for all photosynthetic organisms, the organelle genomes of both photosynthetic and non-photosynthetic organisms (fungi, algae, and protozoa) and plant viruses." At present, the searchable database contains "more than 20,000 genes, which can be translated into proteins, organized into about 2,000 gene families based on their sequence homology." Typical entries include gene family number and gene family name, "Gene & Gene Product descriptions & synonyms, and Accession numbers with links to SWISS-PROT & EMBL."

459

Phase Equilibria Diagrams Database  

National Institute of Standards and Technology Data Gateway

SRD 31 NIST/ACerS Phase Equilibria Diagrams Database (PC database for purchase)   The Phase Equilibria Diagrams Database contains commentaries and more than 21,000 diagrams for non-organic systems, including those published in all 21 hard-copy volumes produced as part of the ACerS-NIST Phase Equilibria Diagrams Program (formerly titled Phase Diagrams for Ceramists): Volumes I through XIV (blue books); Annuals 91, 92, 93; High Tc Superconductors I & II; Zirconium & Zirconia Systems; and Electronic Ceramics I. Materials covered include oxides as well as non-oxide systems such as chalcogenides and pnictides, phosphates, salt systems, and mixed systems of these classes.

460

The Press Freedom Database  

NSDL National Science Digital Library

Developed by the Committee to Protect Journalists (CPJ), The Press Freedom Database contains case histories of documented press freedom violations against journalists and media organizations worldwide as well as annual CPJ reports on the violations in specific countries and regions. The case histories document the circumstances in which journalists have been attacked, killed, expelled, censored, harassed, threatened, and/or imprisoned. The database is searchable by journalist name, news organization, type of organization, date, country, or region. Currently, the database, which is updated weekly, contains over 2,000 reports of press freedom violations, spanning from 1993 to the present.

461

Nuclear structure database  

SciTech Connect

A nuclear structure database has been created from the Table of Isotopes level-scheme file. This database contains evaluated data (through 1977) on level and deexcitation properties for all known isotopes from radioactive decay and nuclear reaction studies. The data are organized in simple array formats to enable rapid searches for specific level or decay information. Examples of the use of this database to study the properties of first excited J/sup ..pi../ = 2/sup +/ states in even-even nuclei and Weisskopf enhancements of delayed ..gamma..-ray transitions are shown. 6 figures, 3 tables.

Firestone, R.B.; Browne, E.

1980-06-01

462

Carbon Capture and Storage Database (CCS) from DOE's National Energy Technology Laboratory (NETL)  

DOE Data Explorer

NETL's Carbon Capture and Storage (CCS) Database includes active, proposed, canceled, and terminated CCS projects worldwide. Information in the database regarding technologies being developed for capture, evaluation of sites for carbon dioxide (CO2) storage, estimation of project costs, and anticipated dates of completion is sourced from publically available information. The CCS Database provides the public with information regarding efforts by various industries, public groups, and governments towards development and eventual deployment of CCS technology. The database contains more than 260 CCS projects worldwide in more than 30 countries across 6 continents. Access to the database requires use of Google Earth, as the NETL CCS database is a layer in Google Earth. Or, users can download a copy of the database in MS-Excel directly from the NETL website.

463

Data Mining Diabetic Databases: Are Rough Sets a Useful Addition?  

Microsoft Academic Search

The publicly available Pima Indian diabetic database (PIDD) at the UC- Irvine Machine Learning Lab has become a standard for testing data mining algorithms to see their accuracy in predicting diabetic status from the 8 variables given. Looking at the 392 complete cases, guessing all are non-diabetic gives an accuracy of 65.1%. Since 1988, many dozens of publications using various

Joseph L. Breault

464

Genome analysis of DNA repair genes in the alpha proteobacterium Caulobacter crescentus  

PubMed Central

Background The integrity of DNA molecules is fundamental for maintaining life. The DNA repair proteins protect organisms against genetic damage, by removal of DNA lesions or helping to tolerate them. DNA repair genes are best known from the gamma-proteobacterium Escherichia coli, which is the most understood bacterial model. However, genome sequencing raises questions regarding uniformity and ubiquity of these DNA repair genes and pathways, reinforcing the need for identifying genes and proteins, which may respond to DNA damage in other bacteria. Results In this study, we employed a bioinformatic approach, to analyse and describe the open reading frames potentially related to DNA repair from the genome of the alpha-proteobacterium Caulobacter crescentus. This was performed by comparison with known DNA repair related genes found in public databases. As expected, although C. crescentus and E. coli bacteria belong to separate phylogenetic groups, many of their DNA repair genes are very similar. However, some important DNA repair genes are absent in the C. crescentus genome and other interesting functionally related gene duplications are present, which do not occur in E. coli. These include DNA ligases, exonuclease III (xthA), endonuclease III (nth), O6-methylguanine-DNA methyltransferase (ada gene), photolyase-like genes, and uracil-DNA-glycosylases. On the other hand, the genes imuA and imuB, which are involved in DNA damage induced mutagenesis, have recently been described in C. crescentus, but are absent in E. coli. Particularly interesting are the potential atypical phylogeny of one of the photolyase genes in alpha-proteobacteria, indicating an origin by horizontal transfer, and the duplication of the Ada orthologs, which have diverse structural configurations, including one that is still unique for C. crescentus. Conclusion The absence and the presence of certain genes are discussed and predictions are made considering the particular aspects of the C. crescentus among other known DNA repair pathways. The observed differences enlarge what is known for DNA repair in the Bacterial world, and provide a useful framework for further experimental studies in this organism. PMID:17352799

Martins-Pinheiro, Marinalva; Marques, Regina CP; Menck, Carlos FM

2007-01-01

465

The AGN Black Hole Mass Database  

NASA Astrophysics Data System (ADS)

The AGN Black Hole Mass Database is a compilation of all published spectroscopic reverberation-mapping studies of active galaxies. We have created a public Web interface where users may get the most up-to-date black hole masses from reverberation mapping for any particular active galactic nucleus (AGN), as well as obtain the individual measurements upon which the masses are based and the appropriate references. While the database currently focuses on the measurements necessary for black hole mass determinations, we also plan to expand it in the future to include additional useful information, such as host-galaxy characteristics. New reverberation mapping results will also be incorporated into the database as they are published in peer-refereed journals.

Bentz, Misty C.; Katz, Sarah

2015-01-01

466

gender Inn: Women's and Gender Studies Database  

NSDL National Science Digital Library

This searchable bibliographic database contains records describing over 5,000 works on "feminist theory, feminist literary criticism and gender studies focusing on English and American literature" from 1950 to the present. The search form is available under the heading Research, where users may indicate which field to search, limit by year of publication, and specify whether to return results in English or German. Works included in the data